Mercurial > repos > jfb > difference_finder
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Commonality and Difference finderMADE 7 TO 7 1-15-2019.R Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,1281 @@ +#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon +#the output files have both Y and xY, they shouldn't why is that happening? make it not happen +#make sure that accession numbers stay locked to each motif, somehow +#output should look just like the KALIP input + +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" +#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) +Are_You_Looking_For_Commonality<-"NO" + + +#put the names of your input files here +FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) +Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +#then put the names of your output files here +Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" +Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" + +# Shared_motifs_table<-"Shared motifs 7-27-17.csv" +# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" + +First_unshared_motifs_table<-"R1 substrates.csv" +First_unshared_subbackfreq<-"R1 SBF.csv" + +Second_unshared_motifs_table<-"R2 subs.csv" +Second_unshared_subbackfreq<-"R2 SBf.csv" + +Third_unshared_motifs_table<-"R3 subs.csv" +Third_unshared_subbackfreq<-"R3 SBF.csv" + +#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around +#other languages to see if any of them can do it. +#################################################################################################################################### + + + + + +FirstxY<-rep("xY",times=nrow(FirstSubstrateSet)) +FirstSubstrateSet[,11]<-FirstxY + +SecondxY<-rep("xY",times=nrow(SecondSubstrateSet)) +SecondSubstrateSet[,11]<-SecondxY + +ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet)) +ThirdSubstrateSet[,11]<-ThirdxY + + + + + + + + + + + +#################################################################################################################################### +#################################################################################################################################### +# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two +# separate proteins thus two separate accession numbers? +# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second +# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### + +#Create the motif sets, deciding wether or not you're looking for truncated or full here +#full only +if (Are_You_Looking_For_Commonality=="YES"){ + if (FullMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + leftspaces<-c() + rightspaces<-c() + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + } + + } + # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] + # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) + # + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + + } + } + + } + + ##############################################3 + #Truncated only + if (TruncatedMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + D835Ymotifs[i,1]<-D835letters + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + ITDmotifs[i,1]<-ITDletters + } + } + + } + + ############################################### + #ALL motifs, full and truncated + + if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + leftspaces<-c() + rightspaces<-c() + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + } + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + + #now look for either commonality or difference. Actually could you look for both... + + if (Are_You_Looking_For_Commonality=="YES"){ + + columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Shared_subbackfreq_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + FirstOverlapmotifs<-c() + for (i in 1:nrow(ITDmotifs)){ + for (j in 1:nrow(D835Ymotifs)){ + if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){ + if (ITDmotifs[i,1]==D835Ymotifs[j,1]){ + FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1]) + } + } + } + } + + AllAccessionNumbers<-c() + columnalheader<-c(rep(NA,36)) + FinalMatrix<-matrix(data =columnalheader,nrow = 1) + + FinalMotifs<-c(rep(NA,20)) + FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1) + + + for (l in 1:length(FirstOverlapmotifs)) { + AccessionNumber<-00000000000 + for (k in 1:nrow(FTLwtmotifs)) { + AccessionNumber<-0000000000000 + if(is.na(FTLwtmotifs[k])!=TRUE){ + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) { + substratematrix<-FirstSubstrateSet[k,1:20] + substratematrix<-as.matrix(substratematrix,nrow=1) + FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix) + #when you find a match between the venn diagrams, save the substrate info you get into a matrix + + AccessionNumber <- as.character(FirstSubstrateSet[k, 3]) + #then take the accession number + + for (m in 1:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = AccessionNumber, + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FinalMatrix<-rbind(FinalMatrix,outputmatrix) + } + } + } + } + } + } + + + TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),] + TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),] + + TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),] + TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),] + + write.table( + x = TrueFinalMotifsMatrix, + file = Shared_motifs_table, + quote = FALSE, + sep = ",", + row.names = FALSE, + col.names = TRUE, + na = "", + append = TRUE + ) + + + write.table( + x = TrueMatrix, + file = Shared_subbackfreq_table, + quote = FALSE, + sep = ",", + row.names = FALSE, + col.names = FALSE, + na = "", + append = TRUE + ) + } +} + +if (Are_You_Looking_For_Commonality=="NO"){ + if (FullMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet)) + FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + leftspaces<-c() + rightspaces<-c() + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i]<-FTLwtletters + FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3] + } + + } + # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] + # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) + # + + D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet)) + D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i]<-D835letters + D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3] + } + } + + ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) + ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i]<-ITDletters + ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] + + } + } + names(ITDmotifs)<-ITDAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(FTLwtmotifs)<-FTLwtAccessionNumbers + } + + + ##############################################3 + #Truncated only + if (TruncatedMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + i=2 + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + D835Ymotifs[i,1]<-D835letters + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + ITDmotifs[i,1]<-ITDletters + } + } + names(FTLwtmotifs)<-FTLwtAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(ITDmotifs)<-ITDAccessionNumbers + } + + ############################################### + #ALL motifs, full and truncated + + if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + leftspaces<-c() + rightspaces<-c() + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + names(FTLwtmotifs)<-FTLwtAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(ITDmotifs)<-ITDAccessionNumbers + } + + + FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] + FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] + FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] + + + ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] + ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] + ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] + + + D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] + D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] + D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] + + + columnalheader<-c(rep(NA,35)) + FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(FTLwtmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(FTLwtmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) + } + } + } + FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] + + columnalheader<-c(rep(NA,35)) + ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(ITDmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Thirdsubbackfreq)) { + AN <- as.character(Thirdsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(ITDmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Thirdsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) + } + } + } + ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] + + columnalheader<-c(rep(NA,35)) + D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(D835YmotifsFINAL)) { + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Secondsubbackfreq)) { + AN <- as.character(Secondsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(D835YmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Secondsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) + } + } + } + D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] + + FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) + + + write.table(x=FTLoutputmatrix, + file=First_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=FTLFinalMatrix, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + ############################################################################################################ + + D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) + + write.table(x=D835Youtputmatrix, + file=Second_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=D835YFinalMatrix, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + ############################################################################################################ + + ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) + + write.table(x=ITDoutputmatrix, + file=Third_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Third_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=ITDFinalMatrix, + file=Third_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +} + +# if (Are_You_Looking_For_Commonality=="NO"){ +# +# +# FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers) +# ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers) +# D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers) +# # ?duplicated +# +# FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] +# FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] +# FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1) +# +# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] +# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] +# ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1) +# +# D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] +# D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] +# D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1) +# +# FTLnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(FTLwtmotifsFINAL)) { +# for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) { +# if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE) +# if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){ +# FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(FTLnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Firstsubbackfreq)) { +# AN <- as.character(Firstsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = FTLnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Firstsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) +# } +# } +# } +# ITDnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(ITDmotifsFINAL)) { +# for (w in 1:nrow(ITDmotifsFULLMATRIX)) { +# if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE) +# if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){ +# ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(ITDnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Thirdsubbackfreq)) { +# AN <- as.character(Thirdsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = ITDnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Thirdsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) +# } +# } +# } +# +# +# D835YnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(D835YmotifsFINAL)) { +# for (w in 1:nrow(D835YmotifsFULLMATRIX)) { +# if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE) +# if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){ +# D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(D835YnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Secondsubbackfreq)) { +# AN <- as.character(Secondsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = D835YnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Secondsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) +# } +# } +# } +# +# +# +# # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] +# # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] +# # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers))) +# # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs) +# # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers) +# # TRUEFTLoutputmatrix +# +# write.table(x=FTLwtmotifsFINAL, +# file=First_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=First_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=FTLFinalMatrix, +# file=First_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# +# +# +# +# +# +# write.table(x=D835YmotifsFINAL, +# file=Second_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=Second_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=D835YFinalMatrix, +# file=Second_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# write.table(x=ITDmotifsFINAL, +# file=Third_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=ITDFinalMatrix, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Commonality and Difference finderMADE 7 TO 7.R Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,1281 @@ +#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon +#the output files have both Y and xY, they shouldn't why is that happening? make it not happen +#make sure that accession numbers stay locked to each motif, somehow +#output should look just like the KALIP input + +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" +#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) +Are_You_Looking_For_Commonality<-"YES" + + +#put the names of your input files here +FirstSubstrateSet<- read.csv("Galaxy63-BTK_PLUS-R1_Substrates.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("Galaxy64-BTK_PLUS-R1_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +SecondSubstrateSet<- read.csv("Galaxy65-BTK_PLUS_R2_Substrates.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("Galaxy66-BTK_PLUS_R2_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) +Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +#then put the names of your output files here +Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" +Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" + +# Shared_motifs_table<-"Shared motifs 7-27-17.csv" +# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" + +First_unshared_motifs_table<-"R1 substrates.csv" +First_unshared_subbackfreq<-"R1 SBF.csv" + +Second_unshared_motifs_table<-"R2 subs.csv" +Second_unshared_subbackfreq<-"R2 SBf.csv" + +Third_unshared_motifs_table<-"R3 subs.csv" +Third_unshared_subbackfreq<-"R3 SBF.csv" + +#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around +#other languages to see if any of them can do it. +#################################################################################################################################### + + + + + +FirstxY<-rep("xY",times=nrow(FirstSubstrateSet)) +FirstSubstrateSet[,11]<-FirstxY + +SecondxY<-rep("xY",times=nrow(SecondSubstrateSet)) +SecondSubstrateSet[,11]<-SecondxY + +ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet)) +ThirdSubstrateSet[,11]<-ThirdxY + + + + + + + + + + + +#################################################################################################################################### +#################################################################################################################################### +# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two +# separate proteins thus two separate accession numbers? +# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second +# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### + +#Create the motif sets, deciding wether or not you're looking for truncated or full here +#full only +if (Are_You_Looking_For_Commonality=="YES"){ + if (FullMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + leftspaces<-c() + rightspaces<-c() + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + } + + } + # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] + # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) + # + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + + } + } + + } + + ##############################################3 + #Truncated only + if (TruncatedMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + D835Ymotifs[i,1]<-D835letters + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + ITDmotifs[i,1]<-ITDletters + } + } + + } + + ############################################### + #ALL motifs, full and truncated + + if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + leftspaces<-c() + rightspaces<-c() + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + } + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + ############################################################################################################################# + + #now look for either commonality or difference. Actually could you look for both... + + if (Are_You_Looking_For_Commonality=="YES"){ + + columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Shared_subbackfreq_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + FirstOverlapmotifs<-c() + for (i in 1:nrow(ITDmotifs)){ + for (j in 1:nrow(D835Ymotifs)){ + if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){ + if (ITDmotifs[i,1]==D835Ymotifs[j,1]){ + FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1]) + } + } + } + } + + AllAccessionNumbers<-c() + columnalheader<-c(rep(NA,36)) + FinalMatrix<-matrix(data =columnalheader,nrow = 1) + + FinalMotifs<-c(rep(NA,20)) + FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1) + + + for (l in 1:length(FirstOverlapmotifs)) { + AccessionNumber<-00000000000 + for (k in 1:nrow(FTLwtmotifs)) { + AccessionNumber<-0000000000000 + if(is.na(FTLwtmotifs[k])!=TRUE){ + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) { + substratematrix<-FirstSubstrateSet[k,1:20] + substratematrix<-as.matrix(substratematrix,nrow=1) + FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix) + #when you find a match between the venn diagrams, save the substrate info you get into a matrix + + AccessionNumber <- as.character(FirstSubstrateSet[k, 3]) + #then take the accession number + + for (m in 1:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = AccessionNumber, + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FinalMatrix<-rbind(FinalMatrix,outputmatrix) + } + } + } + } + } + } + + + TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),] + TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),] + + TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),] + TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),] + + write.table( + x = TrueFinalMotifsMatrix, + file = Shared_motifs_table, + quote = FALSE, + sep = ",", + row.names = FALSE, + col.names = TRUE, + na = "", + append = TRUE + ) + + + write.table( + x = TrueMatrix, + file = Shared_subbackfreq_table, + quote = FALSE, + sep = ",", + row.names = FALSE, + col.names = FALSE, + na = "", + append = TRUE + ) + } +} + +if (Are_You_Looking_For_Commonality=="NO"){ + if (FullMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet)) + FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + leftspaces<-c() + rightspaces<-c() + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i]<-FTLwtletters + FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3] + } + + } + # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)] + # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1) + # + + D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet)) + D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i]<-D835letters + D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3] + } + } + + ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) + ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i]<-ITDletters + ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] + + } + } + names(ITDmotifs)<-ITDAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(FTLwtmotifs)<-FTLwtAccessionNumbers + } + + + ##############################################3 + #Truncated only + if (TruncatedMotifsOnly_questionmark=="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + i=2 + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + D835Ymotifs[i,1]<-D835letters + } + } + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + ITDmotifs[i,1]<-ITDletters + } + } + names(FTLwtmotifs)<-FTLwtAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(ITDmotifs)<-ITDAccessionNumbers + } + + ############################################### + #ALL motifs, full and truncated + + if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + + ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,4:18] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + leftspaces<-c() + rightspaces<-c() + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + names(FTLwtmotifs)<-FTLwtAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + names(ITDmotifs)<-ITDAccessionNumbers + } + + + FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] + FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] + FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] + + + ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] + ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] + ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] + + + D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] + D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] + D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] + + + columnalheader<-c(rep(NA,35)) + FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(FTLwtmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(FTLwtmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) + } + } + } + FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] + + columnalheader<-c(rep(NA,35)) + ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(ITDmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Thirdsubbackfreq)) { + AN <- as.character(Thirdsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(ITDmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Thirdsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) + } + } + } + ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] + + columnalheader<-c(rep(NA,35)) + D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(D835YmotifsFINAL)) { + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Secondsubbackfreq)) { + AN <- as.character(Secondsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(D835YmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Secondsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) + } + } + } + D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] + + FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) + + + write.table(x=FTLoutputmatrix, + file=First_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=FTLFinalMatrix, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + ############################################################################################################ + + D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) + + write.table(x=D835Youtputmatrix, + file=Second_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=D835YFinalMatrix, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + ############################################################################################################ + + ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) + + write.table(x=ITDoutputmatrix, + file=Third_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Third_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=ITDFinalMatrix, + file=Third_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +} + +# if (Are_You_Looking_For_Commonality=="NO"){ +# +# +# FTLwtmotifsFULLMATRIX<-cbind(FTLwtmotifs,FTLwtAccessionNumbers) +# ITDmotifsFULLMATRIX<-cbind(ITDmotifs,ITDAccessionNumbers) +# D835YmotifsFULLMATRIX<-cbind(D835Ymotifs,D835YAccessionNumbers) +# # ?duplicated +# +# FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] +# FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs] +# FTLwtmotifsFINAL<-matrix(data=FTLwtmotifsFINAL, ncol = 1) +# +# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs] +# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs] +# ITDmotifsFINAL<-matrix(data=ITDmotifsFINAL, ncol = 1) +# +# D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] +# D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs] +# D835YmotifsFINAL<-matrix(data=D835YmotifsFINAL, ncol = 1) +# +# FTLnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(FTLwtmotifsFINAL)) { +# for (w in 1:nrow(FTLwtmotifsFULLMATRIX)) { +# if (is.na(FTLwtmotifsFULLMATRIX[w,1])!=TRUE) +# if (FTLwtmotifsFINAL[z]==FTLwtmotifsFULLMATRIX[w,1]){ +# FTLnondupeAccessionNumbers<-c(FTLnondupeAccessionNumbers,FTLwtmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# FTLnondupeAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(FTLnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Firstsubbackfreq)) { +# AN <- as.character(Firstsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = FTLnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Firstsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) +# } +# } +# } +# ITDnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(ITDmotifsFINAL)) { +# for (w in 1:nrow(ITDmotifsFULLMATRIX)) { +# if (is.na(ITDmotifsFULLMATRIX[w,1])!=TRUE) +# if (ITDmotifsFINAL[z]==ITDmotifsFULLMATRIX[w,1]){ +# ITDnondupeAccessionNumbers<-c(ITDnondupeAccessionNumbers,ITDmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# ITDnondupeAccessionNumbers<-ITDnondupeAccessionNumbers[!duplicated(ITDnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(ITDnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Thirdsubbackfreq)) { +# AN <- as.character(Thirdsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = ITDnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Thirdsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) +# } +# } +# } +# +# +# D835YnondupeAccessionNumbers<-c() +# +# for (z in 1:nrow(D835YmotifsFINAL)) { +# for (w in 1:nrow(D835YmotifsFULLMATRIX)) { +# if (is.na(D835YmotifsFULLMATRIX[w,1])!=TRUE) +# if (D835YmotifsFINAL[z]==D835YmotifsFULLMATRIX[w,1]){ +# D835YnondupeAccessionNumbers<-c(D835YnondupeAccessionNumbers,D835YmotifsFULLMATRIX[w,2]) +# } +# } +# } +# +# +# #find accession numbers here, put a matrix of those things, amino acid %, but only after I've unduped them +# D835YnondupeAccessionNumbers<-D835YnondupeAccessionNumbers[!duplicated(D835YnondupeAccessionNumbers)] +# +# columnalheader<-c(rep(NA,35)) +# D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) +# +# for (k in 1:length(D835YnondupeAccessionNumbers)) { +# #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is +# #destroyed immediately after use +# for (m in 1:ncol(Secondsubbackfreq)) { +# AN <- as.character(Secondsubbackfreq[1, m]) +# if (grepl(pattern = AN, +# x = D835YnondupeAccessionNumbers[k], +# fixed = TRUE) == TRUE) { +# outputmatrix <- as.character(Secondsubbackfreq[, m]) +# outputmatrix <- matrix(outputmatrix, nrow = 1) +# #with that accession number, find a match in the subbackfreq file and save it here +# D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) +# } +# } +# } +# +# +# +# # FinalFTLmotifs<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] +# # FinalFTLAccessionNumbers<-FTLnondupeAccessionNumbers[!duplicated(FTLnondupeAccessionNumbers)] +# # necessaryNAs<-rep(NA,times=(length(FinalFTLmotifs)-length(FinalFTLAccessionNumbers))) +# # FinalFTLAccessionNumbers<-c(FinalFTLAccessionNumbers,necessaryNAs) +# # TRUEFTLoutputmatrix<-cbind(FinalFTLmotifs,FinalFTLAccessionNumbers) +# # TRUEFTLoutputmatrix +# +# write.table(x=FTLwtmotifsFINAL, +# file=First_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=First_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=FTLFinalMatrix, +# file=First_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# +# +# +# +# +# +# write.table(x=D835YmotifsFINAL, +# file=Second_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=Second_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=D835YFinalMatrix, +# file=Second_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# write.table(x=ITDmotifsFINAL, +# file=Third_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c("Accession Numbers",as.character(Thirdsubbackfreq[1:35,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# write.table(x=ITDFinalMatrix, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# +# +# +# +# +# }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,348 @@ +#I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon +#the output files have both Y and xY, they shouldn't why is that happening? make it not happen +#make sure that accession numbers stay locked to each motif, somehow +#output should look just like the KALIP input + +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" +#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) +Are_You_Looking_For_Commonality<-"NO" + + +#put the names of your input files here +FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE) + +SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE) + +# ThirdSubstrateSet<- read.csv("Galaxy69-BTK_PLUS_R3_Substrates.csv", stringsAsFactors=FALSE) +# Thirdsubbackfreq<- read.csv("Galaxy70-BTK_PLUS_R3_SubstrateBackgroundFrequency.csv", header=FALSE, stringsAsFactors=FALSE) + +#then put the names of your output files here +# Shared_motifs_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-substrates.csv" +# Shared_subbackfreq_table<-"180719_GALAXY-BTK-plus-rep-OVLP-7to7-SubBackFreq.csv" + +# Shared_motifs_table<-"Shared motifs 7-27-17.csv" +# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv" + +First_unshared_motifs_table<-"1R1 substrates.csv" +First_unshared_subbackfreq<-"1R1 SBF.csv" + +Second_unshared_motifs_table<-"1R2 subs.csv" +Second_unshared_subbackfreq<-"1R2 SBf.csv" + +# Third_unshared_motifs_table<-"R3 subs.csv" +# Third_unshared_subbackfreq<-"R3 SBF.csv" + +#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around +#other languages to see if any of them can do it. +#################################################################################################################################### + + + + + +# grepl(pattern = "S", x=asdf, ignore.case = TRUE) + +FirstCentralLetters<-FirstSubstrateSet[,11] +SecondCentralLetters<-SecondSubstrateSet[,11] + +FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) +FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) +FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) + +SecondEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) +SecondTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) +SecondWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) + +FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") +FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") +FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") + +SecondCentralLetters<-replace(SecondCentralLetters,FirstEsses,"xS") +SecondCentralLetters<-replace(SecondCentralLetters,FirstTees,"xT") +SecondCentralLetters<-replace(SecondCentralLetters,FirstWys,"xY") + +#################################################################################################################################### +#################################################################################################################################### +# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two +# separate proteins thus two separate accession numbers? +# It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second +# accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### +#################################################################################################################################### + +#Create the motif sets, deciding wether or not you're looking for truncated or full here +#full only + + +if (Are_You_Looking_For_Commonality=="NO"){ + + ############################################### + #ALL motifs, full and truncated + + if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FTLwtletters<-FirstSubstrateSet[i,4:18] + FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] + FTLwtletters<-paste(FTLwtletters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FTLwtletters<-motif + FTLwtmotifs[i,1]<-FTLwtletters + FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + D835letters<-SecondSubstrateSet[i,4:18] + D835letters<-D835letters[D835letters !="XXXXX"] + D835letters<-paste(D835letters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(D835letters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { + leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + D835letters<-motif + D835Ymotifs[i,1]<-D835letters + D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + + names(FTLwtmotifs)<-FTLwtAccessionNumbers + names(D835Ymotifs)<-D835YAccessionNumbers + + } + + + FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] + FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] + + D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] + D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] + + + columnalheader<-c(rep(NA,36)) + FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(FTLwtmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(FTLwtmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) + } + } + } + FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] + FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] + + columnalheader<-c(rep(NA,36)) + D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) + + for (k in 1:length(D835YmotifsFINAL)) { + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Secondsubbackfreq)) { + AN <- as.character(Secondsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(D835YmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Secondsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) + } + } + } + D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] + D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),] + + FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) + + + FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") + # FLTheader<-unlist(FLTheader) + lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) + righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix)) + FLTaccessionset<-FTLoutputmatrix[,2] + FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "") + FTLmeat<-sapply(FTLmeat, unlist) + colnames(FTLmeat)<-NULL + FTLmeat<-t(FTLmeat) + + FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT) + colnames(FTLoutputmatrix2)<-NULL + rownames(FTLoutputmatrix2)<-NULL + colnames(FLTheader)<-NULL + rownames(FLTheader)<-NULL + + + FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11] + + FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) + FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) + FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) + + FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS") + FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT") + FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY") + + FirstCentralLettersAGAIN->FTLoutputmatrix2[,11] + + FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2) + + write.table(x=FTLoutputmatrix2, + file=First_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=FTLFinalMatrix, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + ############################################################################################################ + + D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) + + D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite") + # D835Yheader<-unlist(D835Yheader) + lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) + righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix)) + D835Yaset<-D835Youtputmatrix[,2] + D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "") + D835meat<-sapply(D835meat, unlist) + colnames(D835meat)<-NULL + D835meat<-t(D835meat) + + D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835) + colnames(D835Youtputmatrix2)<-NULL + rownames(D835Youtputmatrix2)<-NULL + colnames(D835Yheader)<-NULL + rownames(D835Yheader)<-NULL + + + SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11] + + SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE) + SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE) + SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE) + + SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,FirstEsses,"xS") + SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,FirstTees,"xT") + SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,FirstWys,"xY") + + SecondCentralLettersAGAIN->D835Youtputmatrix2[,11] + + D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2) + + write.table(x=D835Youtputmatrix2, + file=Second_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + columnalheader<-c("Accession Numbers",as.character(Firstsubbackfreq[1:35,1])) + columnalheader<-matrix(columnalheader,nrow = 1) + write.table(x=columnalheader, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + + write.table(x=D835YFinalMatrix, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,547 @@ +#Difference finder for only 2 + +#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps +FullMotifsOnly_questionmark<-"NO" +#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps +TruncatedMotifsOnly_questionmark<-"NO" + +FirstSubstrateSet<- read.csv("170922-BTK-MINUS-COMBO FILES_Substrates.csv", stringsAsFactors=FALSE) +Firstsubbackfreq<- read.csv("170922-BTK-MINUS-COMBO FILES_Substrates.csv", header=FALSE, stringsAsFactors=FALSE) + +SecondSubstrateSet<- read.csv("170922-btk-rep OVLP-plus_Substrates.csv", stringsAsFactors=FALSE) +Secondsubbackfreq<- read.csv("170922-btk-rep OVLP-plus_SubBackFreq.csv", header=FALSE, stringsAsFactors=FALSE) + +First_unshared_motifs_table<-"170922-BTK-MINUS-COMBO FILES_Substrates-unique.csv" +First_unshared_subbackfreq<-"170922-BTK-MINUS-COMBO FILES_SubBackFreq-unique.csv" + +Second_unshared_motifs_table<-"170922-btk-rep OVLP-plus_Substrates-unique.csv" +Second_unshared_subbackfreq<-"170922-btk-rep OVLP-plus_SubBackFreq-unique.csv" + + +LeftOfYLetters<-7 +RightOfYLetters<-7 + +if (FullMotifsOnly_questionmark=="YES"){ + FirstMotifs=rep(NA,times=nrow(FirstSubstrateSet)) + FirstAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + leftspaces<-c() + rightspaces<-c() + for (i in 1:nrow(FirstSubstrateSet)){ + FirstLetters<-FirstSubstrateSet[i,7:15] + FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] + FirstLetters<-paste(FirstLetters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FirstLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { + motif<-YYYmotif + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FirstLetters<-motif + FirstMotifs[i]<-FirstLetters + FirstAccessionNumbers[i]<-FirstSubstrateSet[i,3] + } + + } + # FirstMotifs <- FirstMotifs[!is.na(FirstMotifs)] + # FirstMotifs<-matrix(FirstMotifs,ncol = 1) + # + + SecondMotifs=rep(NA,times=nrow(FirstSubstrateSet)) + SecondAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + + for (i in 1:nrow(SecondSubstrateSet)){ + SecondLetters<-SecondSubstrateSet[i,7:15] + SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] + SecondLetters<-paste(SecondLetters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(SecondLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + SecondLetters<-motif + SecondMotifs[i]<-SecondLetters + SecondAccessionNumbers[i]<-SecondSubstrateSet[i,3] + } + } + names(FirstMotifs)<-FirstAccessionNumbers + names(SecondMotifs)<-SecondAccessionNumbers + + +# ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet)) +# ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet)) + if(1==0){ + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,7:15] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) { + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i]<-ITDletters + ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3] + + } + } + } + #names(ITDmotifs)<-ITDAccessionNumbers + names(SecondMotifs)<-SecondAccessionNumbers + names(FirstMotifs)<-FirstAccessionNumbers +} + + +##############################################3 +#Truncated only +if (TruncatedMotifsOnly_questionmark=="YES"){ + FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FirstLetters<-FirstSubstrateSet[i,7:15] + FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] + FirstLetters<-paste(FirstLetters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(FirstLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FirstLetters<-motif + FirstMotifs[i,1]<-FirstLetters + FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + } + + SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + i=2 + for (i in 1:nrow(SecondSubstrateSet)){ + SecondLetters<-SecondSubstrateSet[i,7:15] + SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] + SecondLetters<-paste(SecondLetters, sep="", collapse="") + + + YYYmotif <- unlist(strsplit(SecondLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + SecondLetters<-motif + SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + SecondMotifs[i,1]<-SecondLetters + } + } + +# ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) +# ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + if(1==0){ + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,7:15] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3] + ITDmotifs[i,1]<-ITDletters + } + } + } + names(FirstMotifs)<-FirstAccessionNumbers + names(SecondMotifs)<-SecondAccessionNumbers + #names(ITDmotifs)<-ITDAccessionNumbers +} + +############################################### +#ALL motifs, full and truncated + +if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ + #print("!")} + FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) + + for (i in 1:nrow(FirstSubstrateSet)){ + FirstLetters<-FirstSubstrateSet[i,7:15] + FirstLetters<-FirstLetters[FirstLetters !="XXXXX"] + FirstLetters<-paste(FirstLetters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(FirstLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + + + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FirstLetters<-motif + FirstMotifs[i,1]<-FirstLetters + FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + FirstLetters<-motif + FirstMotifs[i,1]<-FirstLetters + FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + + + } + + } + + SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) + SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) + + for (i in 1:nrow(SecondSubstrateSet)){ + SecondLetters<-SecondSubstrateSet[i,7:15] + SecondLetters<-SecondLetters[SecondLetters !="XXXXX"] + SecondLetters<-paste(SecondLetters, sep="", collapse="") + leftspaces<-c() + rightspaces<-c() + + YYYmotif <- unlist(strsplit(SecondLetters, split = "")) + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + SecondLetters<-motif + SecondMotifs[i,1]<-SecondLetters + SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + SecondLetters<-motif + SecondMotifs[i,1]<-SecondLetters + SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3] + } + } + + + #ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1) + #ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet)) + if(1==0){ + for (i in 1:nrow(ThirdSubstrateSet)){ + ITDletters<-ThirdSubstrateSet[i,7:15] + ITDletters<-ITDletters[ITDletters !="XXXXX"] + ITDletters<-paste(ITDletters, sep="", collapse="") + YYYmotif <- unlist(strsplit(ITDletters, split = "")) + leftspaces<-c() + rightspaces<-c() + YYYposition <- match(x = "x", table = YYYmotif) + #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are + #just 3 letters to the left of x + + YYYLettersToTheLeft <- YYYposition - 1 + #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is + #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 + YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 + #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the + #variable the user puts in is + if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) { + leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft)) + rightspaces<-rep(" ",times=4-(YYYLettersToTheRight)) + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + + if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){ + motif<-YYYmotif + #add blank spaces if the motif has less than 4 letters to the left/right + motif<-c(leftspaces,YYYmotif,rightspaces) + #save that motif, which is the Y and +/- 4 amino acids, including truncation + motif<-motif[!motif %in% "x"] + motif<-paste(motif, sep="", collapse="") + ITDletters<-motif + ITDmotifs[i,1]<-ITDletters + ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] + } + } + } + names(FirstMotifs)<-FirstAccessionNumbers + names(SecondMotifs)<-SecondAccessionNumbers + #names(ITDmotifs)<-ITDAccessionNumbers +} + + +FirstMotifsFINAL<-FirstMotifs[!FirstMotifs %in% SecondMotifs] +#FirstMotifsFINAL<-FirstMotifsFINAL[!FirstMotifsFINAL %in% ITDmotifs] +FirstMotifsFINAL<-FirstMotifsFINAL[!duplicated(FirstMotifsFINAL)] + + +# ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% SecondMotifs] +# ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FirstMotifs] +# ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)] + + +SecondMotifsFINAL<-SecondMotifs[!SecondMotifs %in% FirstMotifs] +#SecondMotifsFINAL<-SecondMotifsFINAL[!SecondMotifsFINAL %in% ITDmotifs] +SecondMotifsFINAL<-SecondMotifsFINAL[!duplicated(SecondMotifsFINAL)] + + +columnalheader<-c(rep(NA,36)) +FirstFinalMatrix<-matrix(data =columnalheader,nrow = 1) + +for (k in 1:length(FirstMotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 2:ncol(Firstsubbackfreq)) { + AN <- as.character(Firstsubbackfreq[2, m]) + #print(AN)} + if (grepl(pattern = AN, + x = names(FirstMotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Firstsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + FirstFinalMatrix<-rbind(FirstFinalMatrix,outputmatrix) + # print(AN,outputmatrix)} + } + } +} +FirstFinalMatrix<-FirstFinalMatrix[!duplicated(FirstFinalMatrix),] + +#columnalheader<-c(rep(NA,36)) +#ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1) + +if(1==0){ + for (k in 1:length(ITDmotifsFINAL)) { + AN<-00000 + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Thirdsubbackfreq)) { + AN <- as.character(Thirdsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(ITDmotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Thirdsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix) + } + } + } + ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),] +} + +columnalheader<-c(rep(NA,36)) +SecondFinalMatrix<-matrix(data =columnalheader,nrow = 1) + +for (k in 1:length(SecondMotifsFINAL)) { + #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is + #destroyed immediately after use + for (m in 1:ncol(Secondsubbackfreq)) { + AN <- as.character(Secondsubbackfreq[1, m]) + if (grepl(pattern = AN, + x = names(SecondMotifsFINAL[k]), + fixed = TRUE) == TRUE) { + outputmatrix <- as.character(Secondsubbackfreq[, m]) + outputmatrix <- matrix(outputmatrix, nrow = 1) + #with that accession number, find a match in the subbackfreq file and save it here + SecondFinalMatrix<-rbind(SecondFinalMatrix,outputmatrix) + } + } +} +SecondFinalMatrix<-SecondFinalMatrix[!duplicated(SecondFinalMatrix),] +FTLoutputmatrix<-matrix(data=c(FirstMotifsFINAL,names(FirstMotifsFINAL)),ncol = 2) + + +write.table(x=FTLoutputmatrix, + file=First_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +columnalheader<-c(as.character(Firstsubbackfreq[1:36,1])) +columnalheader<-matrix(columnalheader,nrow = 1) +write.table(x=columnalheader, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) +FirstFinalMatrix<-FirstFinalMatrix[2:nrow(FirstFinalMatrix),] +write.table(x=FirstFinalMatrix, + file=First_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +############################################################################################################ + +D835Youtputmatrix<-matrix(data=c(SecondMotifsFINAL,names(SecondMotifsFINAL)),ncol = 2) + +write.table(x=D835Youtputmatrix, + file=Second_unshared_motifs_table, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +columnalheader<-c(as.character(Firstsubbackfreq[1:36,1])) +columnalheader<-matrix(columnalheader,nrow = 1) +write.table(x=columnalheader, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) +SecondFinalMatrix<-SecondFinalMatrix[2:nrow(SecondFinalMatrix),] +write.table(x=SecondFinalMatrix, + file=Second_unshared_subbackfreq, + quote=FALSE, sep=",", + row.names=FALSE,col.names = FALSE, na="", append=TRUE) + +############################################################################################################ + +# ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2) +# +# write.table(x=ITDoutputmatrix, +# file=Third_unshared_motifs_table, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# +# columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1])) +# columnalheader<-matrix(columnalheader,nrow = 1) +# write.table(x=columnalheader, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) +# ITDFinalMatrix<-ITDFinalMatrix[2:nrow(ITDFinalMatrix),] +# write.table(x=ITDFinalMatrix, +# file=Third_unshared_subbackfreq, +# quote=FALSE, sep=",", +# row.names=FALSE,col.names = FALSE, na="", append=TRUE) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/differenceFinder.xml Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,49 @@ +<tool id="commonality_r" name="difference_finder" version="1.0.0"> + <description>finds differences</description> + <requirements> + <requirement type="package">R</requirement> + </requirements> + <command><![CDATA[ + ln -s '$input1' S1.csv && + ln -s '$input2' SBF1.csv && + ln -s '$input3' S2.csv && + ln -s '$input4' SBF2.csv && + + Rscript '$__tool_directory__/Difference finderMADE 7 TO 7 1-15-2019.R' + ]]></command> + <inputs> + <param format="csv" name="input1" type="data" label="First Substrate Set"/> + <param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/> + <param format="csv" name="input3" type="data" label="Second Substrate Set"/> + <param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/> + <param name="outGroup" type="text" value="kinase" label="Kinase Name"/> + </inputs> + <outputs> + <data format="csv" name="substrates1" from_work_dir="1R1 substrates.csv" label="${outGroup}_First_Unshared_Substrates.csv"/> + <data format="csv" name="SBF1" from_work_dir="1R1 SBF.csv" label="${outGroup}_First_Unshared_SBF.csv"/> + + <data format="csv" name="substrates2" from_work_dir="1R2 subs.csv" label="${outGroup}_Second_Unshared_Substrates.csv"/> + <data format="csv" name="SBF2" from_work_dir="1R2 SBf.csv" label="${outGroup}_Second_Unshared_SubstratesSBF.csv"/> + </outputs> + <tests> + <test> + <param name="input1.csv" ftype="csv" value="input1.csv"/> + <param name="positives" ftype="csv" value="substrates.csv"/> + <param name="SBF" ftype="csv" value="SBF.csv"/> + <output name="Negatives" file="negatives.csv"/> + </test> + </tests> + <help><![CDATA[ + This tool takes two Kinamine outputs (substrates and substrate background frequency files) and finds the symmetrical differences between those sets + + Let us call the two INPUT substrate files 'Substrates A' and 'Substrates B'. Let us call the two OUTPUT substrate files 'Substrates Y' and 'Substrates Z'. If we treat each file as a SET, then... + + 'Substrates Y' consists of all 'Substrates A' that are not in 'Substrates B'. 'Substrates Z' consists of all 'Substrates B' that are not in 'Substrates A'. + + The associated Substrate Background Frequency files for each consists of all the proteins associated with that substrate file. + ]]></help> + <citations> + <citation type="doi">10.1074/mcp.RA118.001111</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/1R1 SBF.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,88 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|P19338|NUCL_HUMAN,10.140845070422536,0.14084507042253522,10.28169014084507,14.507042253521126,3.6619718309859155,10.985915492957748,0.14084507042253522,2.3943661971830985,12.676056338028168,3.943661971830986,1.1267605633802817,2.9577464788732395,4.366197183098591,1.971830985915493,3.6619718309859155,5.070422535211268,5.352112676056338,5.211267605633803,0.28169014084507044,1.1267605633802817,,39.014084507042256,46.197183098591545,54.50704225352113,24.788732394366196,16.47887323943662,4.929577464788732,6.338028169014084,26.338028169014088,5.070422535211268,10.422535211267606,,74,13,710 +sp|P09651|ROA1_HUMAN,2.956989247311828,0.5376344086021506,4.838709677419355,4.838709677419355,6.182795698924731,25.0,2.1505376344086025,2.1505376344086025,4.838709677419355,2.1505376344086025,1.6129032258064515,5.64516129032258,2.6881720430107525,3.225806451612903,6.720430107526881,11.29032258064516,3.225806451612903,4.56989247311828,0.2688172043010753,5.10752688172043,,50.537634408602145,32.25806451612903,60.752688172043015,9.67741935483871,13.70967741935484,8.870967741935484,4.301075268817205,32.52688172043011,11.559139784946236,14.516129032258064,,54,6,372 +sp|Q32P51|RA1L2_HUMAN,3.4375000000000004,0.9375,5.625,5.3125,6.875000000000001,19.6875,2.5,2.5,5.9375,2.5,1.875,5.3125,3.125,3.4375000000000004,6.875000000000001,10.0,4.375,5.625,0.3125,3.75,,47.5,35.0,58.125,10.9375,15.3125,8.75,5.0,28.75,10.9375,14.375,,46,4,320 +sp|P22626|ROA2_HUMAN,3.1161473087818696,0.28328611898017,4.815864022662889,6.232294617563739,5.382436260623229,24.362606232294617,1.9830028328611897,2.5495750708215295,5.382436260623229,2.8328611898017,1.9830028328611897,5.382436260623229,4.2492917847025495,2.8328611898017,7.0821529745042495,7.0821529745042495,3.39943342776204,4.53257790368272,0.28328611898017,6.232294617563739,,51.55807365439094,33.711048158640224,57.22379603399433,11.048158640226628,14.44759206798867,8.215297450424929,5.38243626062323,32.01133144475921,11.898016997167138,10.48158640226629,,37,9,353 +sp|P60709|ACTB_HUMAN,7.733333333333333,1.6,6.133333333333333,6.933333333333333,3.4666666666666663,7.466666666666668,2.4,7.466666666666668,5.066666666666666,7.199999999999999,4.533333333333333,2.4,5.066666666666666,3.2,4.8,6.666666666666667,6.933333333333333,5.866666666666666,1.0666666666666667,4.0,,50.400000000000006,30.93333333333333,49.86666666666666,13.066666666666666,12.266666666666666,5.6,14.666666666666668,21.066666666666666,8.533333333333333,13.6,,51,15,375 +sp|P63261|ACTG_HUMAN,7.733333333333333,1.6,5.333333333333334,7.733333333333333,3.4666666666666663,7.466666666666668,2.4,7.733333333333333,5.066666666666666,7.199999999999999,4.533333333333333,2.4,5.066666666666666,3.2,4.8,6.666666666666667,6.933333333333333,5.6000000000000005,1.0666666666666667,4.0,,50.400000000000006,30.93333333333333,48.8,13.066666666666666,12.266666666666666,5.6,14.933333333333334,20.8,8.533333333333333,13.6,,51,15,375 +sp|P07195|LDHB_HUMAN,6.287425149700598,1.4970059880239521,5.688622754491018,6.287425149700598,1.4970059880239521,6.88622754491018,2.095808383233533,7.18562874251497,7.784431137724551,10.778443113772456,2.9940119760479043,5.089820359281437,3.293413173652695,3.293413173652695,2.3952095808383236,7.784431137724551,3.8922155688622757,11.377245508982035,1.7964071856287425,2.095808383233533,,52.395209580838326,32.634730538922156,51.796407185628745,11.976047904191617,12.275449101796408,8.383233532934131,17.964071856287426,24.550898203592816,5.389221556886227,11.676646706586826,,39,2,334 +sp|O75746|CMC1_HUMAN,9.587020648967552,1.0324483775811208,4.277286135693215,5.3097345132743365,6.1946902654867255,8.259587020648967,1.9174041297935103,5.752212389380531,5.014749262536873,10.176991150442479,1.4749262536873156,3.687315634218289,5.014749262536873,4.572271386430678,5.3097345132743365,5.752212389380531,5.162241887905605,7.227138643067847,0.5899705014749262,3.687315634218289,,53.98230088495574,30.08849557522124,50.0,9.587020648967552,12.24188790560472,8.259587020648967,15.92920353982301,25.073746312684364,10.47197640117994,10.914454277286136,,74,2,678 +sp|P42166|LAP2A_HUMAN,7.780979827089338,1.440922190201729,5.043227665706052,7.492795389048991,2.7377521613832854,6.195965417867435,1.8731988472622478,4.322766570605188,7.780979827089338,9.510086455331413,1.0086455331412103,3.170028818443804,6.340057636887608,5.043227665706052,4.899135446685879,11.815561959654179,6.051873198847262,5.3314121037463975,0.2881844380403458,1.8731988472622478,,40.48991354466858,35.30259365994236,53.170028818443804,12.536023054755043,14.553314121037465,8.213256484149856,13.8328530259366,19.308357348703172,4.899135446685879,17.86743515850144,,124,4,694 +sp|P11142|HSP7C_HUMAN,7.739938080495357,0.6191950464396285,7.120743034055728,7.5851393188854495,3.7151702786377707,8.204334365325078,1.08359133126935,6.811145510835913,8.359133126934983,6.811145510835913,2.0123839009287927,5.263157894736842,3.8699690402476783,4.024767801857585,4.3343653250774,5.41795665634675,7.275541795665634,7.120743034055728,0.30959752321981426,2.321981424148607,,45.6656346749226,37.77089783281734,52.63157894736842,14.705882352941178,13.777089783281733,9.287925696594428,13.622291021671826,23.065015479876163,6.346749226006192,12.693498452012385,,82,7,646 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+sp|Q93079|H2B1H_HUMAN,10.317460317460316,0.0,3.1746031746031744,4.761904761904762,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,50.793650793650784,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873012,5.555555555555555,17.46031746031746,,22,2,126 +sp|Q5QNW6|H2B2F_HUMAN,9.523809523809524,0.0,3.1746031746031744,4.761904761904762,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,6.349206349206349,7.936507936507936,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,50.79365079365079,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873016,5.555555555555555,17.46031746031746,,22,2,126 +sp|Q99877|H2B1N_HUMAN,9.523809523809524,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.904761904761903,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,39.68253968253968,37.3015873015873,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,22.22222222222222,5.555555555555555,18.253968253968253,,23,2,126 +sp|P57053|H2BFS_HUMAN,10.317460317460316,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.079365079365079,4.761904761904762,2.380952380952381,2.380952380952381,5.555555555555555,2.380952380952381,7.142857142857142,10.317460317460316,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.301587301587304,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873012,5.555555555555555,16.666666666666664,,21,2,126 +sp|Q99879|H2B1M_HUMAN,8.73015873015873,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,5.555555555555555,15.873015873015872,4.761904761904762,2.380952380952381,3.1746031746031744,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,5.555555555555555,7.936507936507936,0.0,3.968253968253968,,40.476190476190474,38.095238095238095,49.2063492063492,7.936507936507937,24.6031746031746,5.555555555555555,10.317460317460316,22.22222222222222,5.555555555555555,16.666666666666664,,21,2,126
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/1R1 substrates.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,293 @@ +Substrate,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,Phosphite +,,sp|Q13283|G3BP1_HUMAN, , , , , , , ,xS,S,S,P,A,P,A,D, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , , ,T,F,xT,A,W,C,N,S,H,L, +,,sp|P19338|NUCL_HUMAN,D,E,E,E,D,D,D,xS,E,E,D,E,E,D,D, +,,sp|Q15738|NSDHL_HUMAN, , ,V,A,L,A,G,xT,F,H,Y,Y,S,C,E, +,,sp|Q9Y371|SHLB1_HUMAN, ,L,A,A,D,A,G,xT,F,L,S,R, , , , +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,S,H,F,E,Q,W,G,xT,L,T,D,C,V,V,M, +,,sp|P54136|SYRC_HUMAN, , , , , , , ,xS,T,I,I,G,E,S,I, +,,sp|P22626|ROA2_HUMAN, , ,G,F,G,F,V,xT,F,S,S,M,A,E,V, +,,sp|Q8NBS9|TXND5_HUMAN, , , , ,G,Y,P,xT,L,L,L,F,R, , , +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, ,T,V,L,S,G,G,xT,T,M,Y,P,G,I,A, +,,sp|Q96JH7|VCIP1_HUMAN, , , , , ,S,S,xT,T,F,F,E,L,Q,E, +,,sp|Q13283|G3BP1_HUMAN, , , , , , ,S,xS,S,P,A,P,A,D,I, +,,sp|P07195|LDHB_HUMAN, , , , , ,G,L,xT,S,V,I,N,Q,K, , +,,sp|Q15007|FL2D_HUMAN, , , , , , ,S,xT,M,V,D,P,A,I,N, +,,sp|O14776|TCRG1_HUMAN, , , , , , ,A,xT,F,S,E,F,A,A,K, +,,sp|O15294|OGT1_HUMAN,L,C,P,T,H,A,D,xS,L,N,N,L,A,N,I, +,,sp|Q9UKX7|NUP50_HUMAN, , , , ,G,I,G,xT,L,H,L,K,P,T,A, +,,sp|O43312|MTSS1_HUMAN, , , ,R,P,A,S,xT,A,G,L,P,T,T,L, +,,sp|P22314|UBA1_HUMAN, , , , , ,L,Q,xT,S,S,V,L,V,S,G, +,,sp|O75746|CMC1_HUMAN, , , , , ,L,A,xT,A,T,F,A,G,I,E, +,,sp|Q15005|SPCS2_HUMAN, ,F,F,D,H,S,G,xT,L,V,M,D,A,Y,E, +,,sp|P62995|TRA2B_HUMAN, , , , ,R,P,H,xT,P,T,P,G,I,Y, , +,,sp|Q13596|SNX1_HUMAN, , ,A,V,G,T,Q,xT,L,S,G,A,G,L,L, +,,sp|P42166|LAP2A_HUMAN,S,D,E,E,R,E,P,xT,P,V,L,G,S,G,A, +,,sp|P22626|ROA2_HUMAN, , , , , , ,V,xT,F,S,S,M,A,E,V, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN, , , , , , ,I,xT,I,T,N,D,K, , , +,,sp|P25789|PSA4_HUMAN, , , , , , ,T,xT,I,F,S,P,E,G,R, +,,sp|Q9Y277|VDAC3_HUMAN, , , ,V,N,N,A,xS,L,I,G,L,G,Y,T, +,,sp|O75521|ECI2_HUMAN,P,F,S,H,L,G,Q,xS,P,E,G,C,S,S,Y, +,,sp|P04075|ALDOA_HUMAN, , , , , ,A,L,xT,F,S,Y,G,R, , , +,,sp|Q14498|RBM39_HUMAN, , , , , ,D,K,xS,P,V,R,E,P,I,D, +,,sp|P42166|LAP2A_HUMAN, ,G,P,P,D,F,S,xS,D,E,E,R,E,P,T, +,,sp|Q9UPN3|MACF1_HUMAN, , , , ,I,S,G,xT,F,S,S,G,W,T,V, +,,sp|P12955|PEPD_HUMAN, , , , , , , ,xS,T,L,F,V,P,R, , +,,sp|P49321|NASP_HUMAN, ,P,E,V,N,G,G,xS,G,D,A,V,P,S,G, +,,sp|Q9ULW0|TPX2_HUMAN, , , , , ,G,C,xT,I,V,K,P,F,N,L, +,,sp|Q13177|PAK2_HUMAN, , ,S,T,M,V,G,xT,P,Y,W,M,A,P,E, +,,sp|P62987|RL40_HUMAN; sp|P62979|RS27A_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; tr|A0A2R8Y422|A0A2R8Y422_HUMAN, , , , , , ,E,xS,T,L,H,L,V,L,R, +,,sp|P17844|DDX5_HUMAN, , , , , , ,T,xT,Y,L,V,L,D,E,A, +,,sp|P12956|XRCC6_HUMAN, , , ,T,F,N,T,xS,T,G,G,L,L,L,P, +,,sp|O15294|OGT1_HUMAN, , , , ,L,C,P,xT,H,A,D,S,L,N,N, +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,K,L,F,I,G,G,L,xS,F,E,T,T,D,E,S, +,,sp|Q9UGU5|HMGX4_HUMAN, , , , , , , ,xS,P,P,T,T,M,L,L, +,,sp|Q15181|IPYR_HUMAN, ,G,I,S,C,M,N,xT,T,L,S,E,S,P,F, +,,sp|Q9NUL3|STAU2_HUMAN, , , , , ,V,I,xS,G,T,T,L,G,Y,L, +,,sp|P24752|THIL_HUMAN, , , ,T,P,I,G,xS,F,L,G,S,L,S,L, +,,sp|P60900|PSA6_HUMAN, , , , , ,H,I,xT,I,F,S,P,E,G,R, +,,sp|P63010|AP2B1_HUMAN; sp|Q10567|AP1B1_HUMAN, , ,L,S,H,A,N,xS,A,V,V,L,S,A,V, +,,sp|Q99832|TCPH_HUMAN,G,D,G,T,T,S,V,xT,L,L,A,A,E,F,L, +,,sp|P53396|ACLY_HUMAN, , , , , ,G,S,xT,F,M,D,H,V,L,R, +,,sp|A0FGR8|ESYT2_HUMAN,G,A,N,T,H,L,S,xT,F,S,F,T,K, , , +,,sp|P49407|ARRB1_HUMAN,A,D,D,T,V,A,P,xS,S,T,F,C,K, , , +,,sp|Q15007|FL2D_HUMAN, , , , , , , ,xS,T,M,V,D,P,A,I, +,,sp|Q96JH7|VCIP1_HUMAN, , , , ,S,S,T,xT,F,F,E,L,Q,E,S, +,,sp|Q99832|TCPH_HUMAN,A,E,V,G,D,G,T,xT,S,V,T,L,L,A,A, +,,sp|Q96I25|SPF45_HUMAN, , , , , , , ,xS,P,T,G,P,S,N,S, +,,sp|O60506|HNRPQ_HUMAN, , ,G,Y,A,F,V,xT,F,C,T,K, , , , +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN, , , , , , ,L,xT,L,H,G,L,Q,Q,Y, +,,sp|Q99832|TCPH_HUMAN,E,V,G,D,G,T,T,xS,V,T,L,L,A,A,E, +,,sp|Q14974|IMB1_HUMAN,A,A,V,E,N,L,P,xT,F,L,V,E,L,S,R, +,,sp|Q8WUA2|PPIL4_HUMAN, , , , ,I,N,E,xT,F,V,D,K,D,F,V, +,,sp|Q16658|FSCN1_HUMAN,V,A,R,P,E,P,A,xT,G,Y,T,L,E,F,R, +,,sp|P31323|KAP3_HUMAN, , , , , ,A,A,xT,I,T,A,T,S,P,G, +,,sp|P10809|CH60_HUMAN,G,D,G,T,T,T,A,xT,V,L,A,R, , , , +,,sp|P20290|BTF3_HUMAN, , , , ,V,Q,A,xS,L,A,A,N,T,F,T, +,,sp|O95319|CELF2_HUMAN, , ,G,C,A,F,V,xT,F,S,T,R, , , , +,,sp|Q13126|MTAP_HUMAN, , , , , ,A,E,xS,F,M,F,R, , , , +,,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN,L,I,N,K,P,D,G,xT,F,L,L,R, , , , +,,sp|Q13177|PAK2_HUMAN, , , , , , ,S,xT,M,V,G,T,P,Y,W, +,,sp|Q9Y2X3|NOP58_HUMAN, ,L,I,A,H,A,G,xS,L,L,N,L,A,K, , +,,sp|P22626|ROA2_HUMAN,F,G,F,V,T,F,S,xS,M,A,E,V,D,A,A, +,,sp|Q9H1E3|NUCKS_HUMAN, , ,A,T,V,T,P,xS,P,V,K,G,K, , , +,,sp|Q13263|TIF1B_HUMAN,A,A,S,A,A,A,A,xS,A,A,S,G,S,P,G, +,,sp|P54136|SYRC_HUMAN, , , , , , ,S,xT,I,I,G,E,S,I,S, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , , , , , ,xT,F,Y,N,E,L,R, , +,,sp|Q08945|SSRP1_HUMAN, , , , ,I,Y,P,xT,F,L,H,L,H,G,K, +,,sp|P53396|ACLY_HUMAN, , , , , , ,G,xS,T,F,M,D,H,V,L, +,,sp|Q01469|FABP5_HUMAN,T,Q,T,V,C,N,F,xT,D,G,A,L,V,Q,H, +,,sp|Q99436|PSB7_HUMAN, , , , , ,T,G,xT,T,I,A,G,V,V,Y, +,,sp|P14314|GLU2B_HUMAN, , , , ,L,G,G,xS,P,T,S,L,G,T,W, +,,sp|Q99436|PSB7_HUMAN, , , , , , , ,xT,T,I,A,G,V,V,Y, +,,sp|P67809|YBOX1_HUMAN,K,E,N,Q,G,D,E,xT,Q,G,Q,Q,P,P,Q, +,,sp|P54105|ICLN_HUMAN, , , , ,G,L,G,xT,G,T,L,Y,I,A,E, +,,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN; sp|Q9H0W9|CK054_HUMAN,K,P,I,G,M,G,G,xT,F,I,I,Q,K, , , +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN,D,L,I,N,N,L,G,xT,I,A,K, , , , , +,,sp|P54819|KAD2_HUMAN,L,Q,A,Y,H,T,Q,xT,T,P,L,I,E,Y,Y, +,,sp|P23193|TCEA1_HUMAN, ,S,A,D,E,P,M,xT,T,F,V,V,C,N,E, +,,sp|P30740|ILEU_HUMAN, , , , , , , ,xT,F,H,F,N,T,V,E, +,,sp|P62995|TRA2B_HUMAN, , ,R,P,H,T,P,xT,P,G,I,Y,M,G,R, +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN, , , ,S,R,P,T,xS,F,A,D,E,L,A,A, +,,sp|P14314|GLU2B_HUMAN, ,L,G,G,S,P,T,xS,L,G,T,W,G,S,W, +,,sp|P49915|GUAA_HUMAN,P,P,T,D,V,T,P,xT,F,L,T,T,G,V,L, +,,sp|P12956|XRCC6_HUMAN, , ,T,F,N,T,S,xT,G,G,L,L,L,P,S, +,,sp|P23528|COF1_HUMAN,T,V,D,D,P,Y,A,xT,F,V,K, , , , , +,,sp|O94826|TOM70_HUMAN, , , , , , ,A,xT,F,Y,L,L,I,G,N, +,,sp|P63220|RS21_HUMAN, , , , , , , ,xT,Y,A,I,C,G,A,I, +,,sp|P62805|H4_HUMAN, , , , , , ,K,xT,V,T,A,M,D,V,V, +,,sp|P55884|EIF3B_HUMAN, , , ,P,R,P,P,xT,L,L,S,Q,E,Q,I, +,,sp|O43312|MTSS1_HUMAN, , , , ,R,P,A,xS,T,A,G,L,P,T,T, +,,sp|O75663|TIPRL_HUMAN, , , , , , ,G,xT,L,L,G,E,S,L,K, +,,sp|P53396|ACLY_HUMAN, , , , ,K,P,A,xS,F,M,T,S,I,C,D, +,,sp|O95619|YETS4_HUMAN, , , , , ,G,V,xT,I,V,K,P,I,V,Y, +,,sp|Q14C86|GAPD1_HUMAN,V,V,S,G,I,S,A,xT,S,E,D,I,P,N,K, +,,sp|P53041|PPP5_HUMAN, , , , , ,L,S,xT,L,V,E,T,T,L,K, +,,sp|P10809|CH60_HUMAN,E,A,G,D,G,T,T,xT,A,T,V,L,A,R, , +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,Q,V,E,H,P,S,V,xT,S,P,L,T,V,E,W, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , , ,T,V,L,xS,G,G,T,T,M,Y,P, +,,sp|P49189|AL9A1_HUMAN, , , , , , ,M,xS,T,G,T,F,V,V,S, +,,sp|P42166|LAP2A_HUMAN, , ,G,P,P,D,F,xS,S,D,E,E,R,E,P, +,,sp|P11021|BIP_HUMAN, ,D,N,H,L,L,G,xT,F,D,L,T,G,I,P, +,,sp|P30626|SORCN_HUMAN, , , , , ,A,L,xT,T,M,G,F,R, , , +,,sp|Q7Z5L9|I2BP2_HUMAN, , , , ,R,P,A,xS,V,S,S,S,A,A,V, +,,sp|O94804|STK10_HUMAN,S,Q,S,R,P,N,S,xS,A,L,E,T,L,G,G, +,,sp|P22314|UBA1_HUMAN, , , ,L,Q,T,S,xS,V,L,V,S,G,L,R, +,,sp|Q13620|CUL4B_HUMAN, , , ,A,F,G,S,xT,I,V,I,N,P,E,K, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN, , , , , , ,T,xT,P,S,Y,V,A,F,T, +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,T,C,Q,V,E,H,P,xS,V,T,S,P,L,T,V, +,,sp|P49407|ARRB1_HUMAN,D,T,V,A,P,S,S,xT,F,C,K, , , , , +,,sp|Q07020|RL18_HUMAN, , , , ,G,C,G,xT,V,L,L,S,G,P,R, +,,sp|P37802|TAGL2_HUMAN, , , , , , , ,xT,L,M,N,L,G,G,L, +,,sp|Q16658|FSCN1_HUMAN,A,P,S,G,P,S,G,xT,L,K, , , , , , +,,sp|Q14156|EFR3A_HUMAN, , , , , , ,L,xT,F,Y,A,V,S,A,P, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN, , , , , , , ,xS,T,E,L,L,I,R, , +,,sp|P22626|ROA2_HUMAN, , , , ,V,T,F,xS,S,M,A,E,V,D,A, +,,sp|O95487|SC24B_HUMAN, , ,D,S,R,P,L,xS,P,I,L,H,I,V,K, +,,sp|P43243|MATR3_HUMAN, , , , , ,L,C,xS,L,F,Y,T,N,E,E, +,,sp|P53396|ACLY_HUMAN, , , ,Y,P,G,S,xT,F,M,D,H,V,L,R, +,,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN; sp|Q6ZRS2|SRCAP_HUMAN,S,P,G,P,S,H,P,xT,F,W,T,Y,T,E,A, +,,sp|Q96T68|SETB2_HUMAN, , , , , , ,G,xT,F,V,C,I,Y,S,G, +,,sp|Q9UIA9|XPO7_HUMAN, , , , , , , ,xT,T,F,Y,T,A,L,G, +,,sp|Q14C86|GAPD1_HUMAN,R,P,S,T,P,G,L,xS,V,V,S,G,I,S,A, +,,sp|P49848|TAF6_HUMAN, , , , , ,F,S,xT,F,I,S,E,G,V,R, +,,sp|P11142|HSP7C_HUMAN,D,I,V,L,V,G,G,xS,T,R, , , , , , +,,sp|O75521|ECI2_HUMAN, , , ,A,T,F,H,xT,P,F,S,H,L,G,Q, +,,sp|P08567|PLEK_HUMAN, , , ,G,S,T,L,xT,S,P,C,Q,D,F,G, +,,sp|Q86UE4|LYRIC_HUMAN,I,P,D,D,Q,K,V,xS,D,D,D,K,E,K,G, +,,sp|P22314|UBA1_HUMAN, , , , ,L,Q,T,xS,S,V,L,V,S,G,L, +,,sp|P62805|H4_HUMAN, , , , , ,T,V,xT,A,M,D,V,V,Y,A, +,,sp|P54886|P5CS_HUMAN, , , , , ,V,G,xT,F,F,S,E,V,K, , +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN, , , , ,S,R,P,xT,S,F,A,D,E,L,A, +,,sp|Q9NYF8|BCLF1_HUMAN, , , , ,L,L,A,xS,T,L,V,H,S,V,K, +,,sp|O75608|LYPA1_HUMAN, , , , , , , ,xT,L,V,N,P,A,N,V, +,,sp|P29350|PTN6_HUMAN, , , ,G,E,P,W,xT,F,L,V,R, , , , +,,sp|O60508|PRP17_HUMAN, ,S,P,S,S,K,P,xS,L,A,V,A,V,D,S, +,,sp|P49407|ARRB1_HUMAN,D,D,T,V,A,P,S,xS,T,F,C,K, , , , +,,sp|Q99832|TCPH_HUMAN,D,A,E,V,G,D,G,xT,T,S,V,T,L,L,A, +,,sp|P55084|ECHB_HUMAN, , , , ,A,A,L,xT,G,L,L,H,R, , , +,,sp|Q99547|MPH6_HUMAN, , , , ,R,Y,E,xT,L,V,G,T,I,G,K, +,,sp|Q15363|TMED2_HUMAN, , , , , , ,Y,xT,F,A,A,H,M,D,G, +,,sp|P53396|ACLY_HUMAN, , , , ,Y,P,G,xS,T,F,M,D,H,V,L, +,,sp|P54819|KAD2_HUMAN, , ,L,Q,A,Y,H,xT,Q,T,T,P,L,I,E, +,,sp|P12956|XRCC6_HUMAN, , , , , , , ,xT,F,N,T,S,T,G,G, +,,sp|P55036|PSMD4_HUMAN, , , , , , ,I,xT,F,C,T,G,I,R, , +,,sp|P62995|TRA2B_HUMAN, , , , ,R,P,H,xT,P,T,P,G,I,Y,M, +,,sp|Q969T9|WBP2_HUMAN, , , , , , ,G,xT,V,Y,L,T,P,Y,R, +,,sp|Q14181|DPOA2_HUMAN, ,S,P,H,Q,L,L,xS,P,S,S,F,S,P,S, +,,sp|Q99832|TCPH_HUMAN, , , , , , ,A,xT,I,S,N,D,G,A,T, +,,sp|P26196|DDX6_HUMAN, , , , , ,G,V,xT,Q,Y,Y,A,Y,V,T, +,,sp|O94804|STK10_HUMAN, , , , ,A,S,Q,xS,R,P,N,S,S,A,L, +,,sp|P09651|ROA1_HUMAN, , , , , ,S,E,xS,P,K,E,P,E,Q,L, +,,sp|Q16629|SRSF7_HUMAN, , , , , , , ,xT,V,W,I,A,R, , , +,,sp|P40926|MDHM_HUMAN, , , , , , ,L,xT,L,Y,D,I,A,H,T, +,,sp|P78527|PRKDC_HUMAN, , , , , ,L,A,xT,T,I,L,Q,H,W,K, +,,sp|P22626|ROA2_HUMAN, , , ,V,T,F,S,xS,M,A,E,V,D,A,A, +,,sp|Q92871|PMM1_HUMAN; sp|O15305|PMM2_HUMAN, , , , , , ,G,xT,F,I,E,F,R, , , +,,sp|P11142|HSP7C_HUMAN,I,V,L,V,G,G,S,xT,R, , , , , , , +,,sp|Q14181|DPOA2_HUMAN, , , , , , , ,xS,P,H,Q,L,L,S,P, +,,sp|O94804|STK10_HUMAN,A,S,Q,S,R,P,N,xS,S,A,L,E,T,L,G, +,,sp|P17844|DDX5_HUMAN, , , , , , , ,xT,T,Y,L,V,L,D,E, +,,sp|Q99832|TCPH_HUMAN, , , , , ,T,C,xT,F,I,L,R, , , , +,,sp|P18124|RL7_HUMAN, , ,Q,I,F,N,G,xT,F,V,K, , , , , +,,tr|A0A1B0GU03|A0A1B0GU03_HUMAN; sp|P07339|CATD_HUMAN, , , , , ,G,I,xT,F,I,A,A,K, , , +,,sp|P47756|CAPZB_HUMAN, , , , , , ,S,xT,L,N,E,I,Y,F,G, +,,sp|Q99436|PSB7_HUMAN, , , , ,T,G,T,xT,I,A,G,V,V,Y,K, +,,sp|O60508|PRP17_HUMAN, , , , , ,S,P,xS,S,K,P,S,L,A,V, +,,sp|P30086|PEBP1_HUMAN, ,N,R,P,T,S,I,xS,W,D,G,L,D,S,G, +,,sp|P62701|RS4X_HUMAN; sp|Q8TD47|RS4Y2_HUMAN, , , , , , ,L,xT,G,V,F,A,P,R, , +,,sp|O43491|E41L2_HUMAN, , , , , ,S,P,xT,K,A,P,H,L,Q,L, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN, , ,I,G,G,I,G,xT,V,P,V,G,R, , , +,,sp|P78527|PRKDC_HUMAN, , , , , ,L,Y,xS,L,A,L,H,P,N,A, +,,sp|Q9NUL3|STAU2_HUMAN, , , ,V,I,S,G,xT,T,L,G,Y,L,S,P, +,,sp|Q13263|TIF1B_HUMAN,A,A,A,A,S,A,A,xS,G,S,P,G,P,G,E, +,,sp|Q99873|ANM1_HUMAN, , , , , , ,A,xT,L,Y,V,T,A,I,E, +,,sp|P55265|DSRAD_HUMAN, , , ,T,L,P,L,xT,G,S,T,F,H,D,Q, +,,sp|P49368|TCPG_HUMAN, , , , , ,A,C,xT,I,L,L,R, , , , +,,sp|Q14C86|GAPD1_HUMAN,T,P,G,L,S,V,V,xS,G,I,S,A,T,S,E, +,,sp|P61158|ARP3_HUMAN,I,V,L,S,G,G,S,xT,M,F,R, , , , , +,,sp|Q13620|CUL4B_HUMAN, , , , ,A,F,G,xS,T,I,V,I,N,P,E, +,,sp|Q00059|TFAM_HUMAN, , , , , ,E,L,xT,L,L,G,K,P,K, , +,,sp|Q15366|PCBP2_HUMAN, , , , ,P,S,S,xS,P,V,I,F,A,G,G, +,,sp|P00338|LDHA_HUMAN, , , , , ,A,D,xT,L,W,G,I,Q,K, , +,,sp|P52209|6PGD_HUMAN, , , , , , , ,xT,I,F,Q,G,I,A,A, +,,sp|Q6PI48|SYDM_HUMAN, , , , ,R,Q,N,xT,F,L,V,L,R, , , +,,sp|Q13283|G3BP1_HUMAN, , , , ,Q,Y,Y,xT,L,L,N,Q,A,P,D, +,,sp|Q13596|SNX1_HUMAN, , , , ,A,V,G,xT,Q,T,L,S,G,A,G, +,,sp|Q15366|PCBP2_HUMAN, , , , , ,P,S,xS,S,P,V,I,F,A,G, +,,sp|O75083|WDR1_HUMAN, , , , , ,L,Y,xS,I,L,G,T,T,L,K, +,,sp|P13861|KAP2_HUMAN, , , , , ,A,A,xT,I,V,A,T,S,E,G, +,,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN, , , , , , ,A,xT,I,A,G,G,G,V,I, +,,sp|P08238|HS90B_HUMAN, , , , , , , ,xT,L,T,L,V,D,T,G, +,,sp|O75534|CSDE1_HUMAN, , , , ,G,T,V,xS,F,H,S,H,S,D,H, +,,sp|Q7Z5L9|I2BP2_HUMAN, ,R,P,A,S,V,S,xS,S,A,A,V,E,H,E, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN, , , , , , , ,xT,F,T,A,W,C,N,S, +,,sp|P00505|AATM_HUMAN, , , , ,I,G,A,xS,F,L,Q,R, , , , +,,sp|P27816|MAP4_HUMAN, , , , , ,S,P,xS,T,L,L,P,K, , , +,,sp|P22626|ROA2_HUMAN,G,F,G,F,V,T,F,xS,S,M,A,E,V,D,A, +,,sp|Q09472|EP300_HUMAN, , , , , ,L,G,xT,F,L,E,N,R, , , +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN, , , , , , , ,xT,T,P,S,Y,V,A,F, +,,sp|P12956|XRCC6_HUMAN, , , , , , ,R,xT,F,N,T,S,T,G,G, +,,sp|Q9BTE3|MCMBP_HUMAN, , , , , , ,N,xS,T,F,T,E,H,L,Y, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN, , ,S,G,E,V,Y,xT,C,Q,V,E,H,P,S, +,,sp|P55265|DSRAD_HUMAN,T,L,P,L,T,G,S,xT,F,H,D,Q,I,A,M, +,,sp|Q9NRW3|ABC3C_HUMAN, , ,A,M,Y,P,G,xT,F,Y,F,Q,F,K, , +,,sp|Q15005|SPCS2_HUMAN, , , ,F,F,D,H,xS,G,T,L,V,M,D,A, +,,sp|Q96JH7|VCIP1_HUMAN, , , , , , ,S,xS,T,T,F,F,E,L,Q, +,,tr|M0R2N4|M0R2N4_HUMAN; sp|Q8WU68|U2AF4_HUMAN; sp|Q01081|U2AF1_HUMAN; sp|P0DN76|U2AF5_HUMAN, , ,D,K,V,N,C,xS,F,Y,F,K, , , , +,,sp|P61158|ARP3_HUMAN,N,I,V,L,S,G,G,xS,T,M,F,R, , , , +,,sp|Q92608|DOCK2_HUMAN, , , , , , ,L,xS,Q,T,F,L,Q,L,S, +,,sp|O14980|XPO1_HUMAN, , , , , , ,E,xT,L,V,Y,L,T,H,L, +,,sp|P18433|PTPRA_HUMAN, , , , , ,T,G,xT,F,C,A,L,S,T,V, +,,sp|Q13347|EIF3I_HUMAN, , , , , ,D,M,xT,M,F,V,T,A,S,K, +,,sp|Q8ND76|CCNY_HUMAN; sp|Q8N7R7|CCYL1_HUMAN, , , , , ,A,S,xT,I,F,L,S,K, , , +,,sp|Q15181|IPYR_HUMAN,G,I,S,C,M,N,T,xT,L,S,E,S,P,F,K, +,,sp|P62805|H4_HUMAN, , , , ,K,T,V,xT,A,M,D,V,V,Y,A, +,,sp|P14625|ENPL_HUMAN,A,D,D,K,Y,N,D,xT,F,W,K, , , , , +,,sp|P82650|RT22_HUMAN, , , , , ,I,L,xT,P,I,I,F,K, , , +,,sp|P14866|HNRPL_HUMAN, , , , ,T,P,A,xS,P,V,V,H,I,R, , +,,sp|Q6UN15|FIP1_HUMAN, ,E,R,D,H,S,P,xT,P,S,V,F,N,S,D, +,,sp|P06748|NPM_HUMAN, , , , , ,L,L,xS,I,S,G,K, , , , +,,sp|P14314|GLU2B_HUMAN, , ,L,G,G,S,P,xT,S,L,G,T,W,G,S, +,,sp|P01911|2B1F_HUMAN; sp|Q30154|DRB5_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,R, +,,sp|P52272|HNRPM_HUMAN,F,G,G,S,F,A,G,xS,F,G,G,A,G,G,H, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,S, +,,sp|O75521|ECI2_HUMAN,A,T,F,H,T,P,F,xS,H,L,G,Q,S,P,E, +,,sp|Q9BTE3|MCMBP_HUMAN, , , , , ,N,S,xT,F,T,E,H,L,Y,R, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , ,A,V,F,P,xS,I,V,G,R, , , , +,,sp|Q86VP6|CAND1_HUMAN, , , , , ,L,G,xT,L,S,A,L,D,I,L, +,,sp|Q08211|DHX9_HUMAN, , , , , ,G,M,xT,L,V,T,P,L,Q,L, +,,sp|Q9Y3I0|RTCB_HUMAN, , , , ,S,S,M,xT,F,L,T,R, , , , +,,sp|Q9BRA2|TXD17_HUMAN, , , , , , , ,xT,I,F,A,Y,F,T,G, +,,sp|P12956|XRCC6_HUMAN, , , , ,T,F,N,xT,S,T,G,G,L,L,L, +,,sp|P43686|PRS6B_HUMAN, , , , ,L,I,F,xS,T,I,T,S,K, , , +,,sp|P54819|KAD2_HUMAN,Q,A,Y,H,T,Q,T,xT,P,L,I,E,Y,Y,R, +,,sp|P27797|CALR_HUMAN, , , , , ,G,Q,xT,L,V,V,Q,F,T,V, +,,sp|Q14697|GANAB_HUMAN, , , , , , ,L,xS,F,Q,H,D,P,E,T, +,,sp|O60508|PRP17_HUMAN, , , , ,S,P,S,xS,K,P,S,L,A,V,A, +,,sp|P51991|ROA3_HUMAN, , , ,W,G,T,L,xT,D,C,V,V,M,R,D, +,,sp|P55884|EIF3B_HUMAN, , , , ,I,S,V,xS,F,Y,H,V,K, , , +,,sp|Q99575|POP1_HUMAN, , , ,Y,I,T,A,xS,T,F,A,Q,A,R, , +,,sp|P15880|RS2_HUMAN, , , , , , ,G,xT,G,I,V,S,A,P,V, +,,sp|P49588|SYAC_HUMAN, , , , , ,I,G,xT,I,Y,G,D,L,K, , +,,sp|Q7Z5L9|I2BP2_HUMAN,R,P,A,S,V,S,S,xS,A,A,V,E,H,E,Q, +,,sp|P25789|PSA4_HUMAN, , , , , , , ,xT,T,I,F,S,P,E,G, +,,sp|Q9UIA9|XPO7_HUMAN, , , , , , ,T,xT,F,Y,T,A,L,G,R, +,,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN,G,T,G,S,G,M,G,xT,L,L,I,S,K, , , +,,sp|O15042|SR140_HUMAN, , , , , ,L,Y,xS,I,L,Q,G,D,S,P, +,,sp|Q9UKM9|RALY_HUMAN, , , , ,G,R,L,xS,P,V,P,V,P,R, , +,,sp|Q13586|STIM1_HUMAN, , ,N,T,L,F,G,xT,F,H,V,A,H,S,S, +,,sp|Q96JH7|VCIP1_HUMAN, , , , , , , ,xS,S,T,T,F,F,E,L, +,,sp|Q7Z5L9|I2BP2_HUMAN, , ,R,P,A,S,V,xS,S,S,A,A,V,E,H, +,,sp|Q8WUK0|PTPM1_HUMAN, , , , , ,D,G,xT,F,V,I,S,K, , , +,,sp|P15498|VAV_HUMAN, , , , ,S,D,G,xT,F,L,V,R, , , , +,,sp|P09651|ROA1_HUMAN; tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN, , , , , ,Y,H,xT,V,N,G,H,N,C,E, +,,sp|Q14C86|GAPD1_HUMAN,L,S,V,V,S,G,I,xS,A,T,S,E,D,I,P, +,,sp|Q9H7N4|SFR19_HUMAN, , , ,Q,R,S,P,xS,P,A,P,A,P,A,P, +,,sp|Q9HCC0|MCCB_HUMAN, , , , ,K,Q,G,xT,I,F,L,A,G,P,P, +,,sp|Q9UI08|EVL_HUMAN, , , ,Y,N,Q,A,xT,P,T,F,H,Q,W,R, +,,sp|Q13283|G3BP1_HUMAN, , , , , ,S,S,xS,P,A,P,A,D,I,A, +,,sp|Q13177|PAK2_HUMAN, , , , , , , ,xS,T,M,V,G,T,P,Y, +,,sp|P20290|BTF3_HUMAN,Q,A,S,L,A,A,N,xT,F,T,I,T,G,H,A, +,,sp|P47756|CAPZB_HUMAN, , , , , , , ,xS,T,L,N,E,I,Y,F, +,,sp|Q13094|LCP2_HUMAN, , ,I,N,Q,D,G,xT,F,L,V,R, , , , +,,sp|Q9H7N4|SFR19_HUMAN, , , , , ,Q,R,xS,P,S,P,A,P,A,P, +,,sp|Q9BWJ5|SF3B5_HUMAN, , , , , , ,Y,xT,I,H,S,Q,L,E,H, +,,sp|P30101|PDIA3_HUMAN,Y,G,V,S,G,Y,P,xT,L,K, , , , , , +,,sp|Q6ZNL6|FGD5_HUMAN, , , ,E,R,P,V,xS,M,S,F,P,L,S,S, +,,sp|P55265|DSRAD_HUMAN, ,T,L,P,L,T,G,xS,T,F,H,D,Q,I,A, +,,sp|O60573|IF4E2_HUMAN, , , , ,Q,I,G,xT,F,A,S,V,E,Q,F, +,,sp|Q8WV74|NUDT8_HUMAN, , , ,A,R,P,A,xS,A,A,V,L,V,P,L, +,,sp|Q15181|IPYR_HUMAN, , , , , ,G,I,xS,C,M,N,T,T,L,S, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , ,A,V,F,P,xS,I,V,G,R,P,R, , +,,sp|Q08945|SSRP1_HUMAN, , , , , ,Q,G,xT,Q,Y,T,F,S,S,I, +,,sp|Q14690|RRP5_HUMAN, , , , , ,A,G,xT,Y,F,S,N,Q,A,V, +,,sp|P07900|HS90A_HUMAN, , , , , , , ,xT,L,T,I,V,D,T,G, +,,sp|O14980|XPO1_HUMAN, ,E,T,L,V,Y,L,xT,H,L,D,Y,V,D,T, +,,sp|P04075|ALDOA_HUMAN,H,E,E,I,A,M,A,xT,V,T,A,L,R, , , +,,sp|O75521|ECI2_HUMAN, , , , , , ,A,xT,F,H,T,P,F,S,H, +,,sp|P23193|TCEA1_HUMAN,S,A,D,E,P,M,T,xT,F,V,V,C,N,E,C, +,,sp|P08865|RSSA_HUMAN,A,S,Y,V,N,L,P,xT,I,A,L,C,N,T,D, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,T,V,L,S,G,G,T,xT,M,Y,P,G,I,A,D, +,,sp|P62807|H2B1C_HUMAN; sp|P57053|H2BFS_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P58876|H2B1D_HUMAN, , , , ,E,S,Y,xS,V,Y,V,Y,K, , , +,,sp|Q15005|SPCS2_HUMAN, , , , , , ,L,xT,F,I,S,G,R, , ,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/1R2 SBf.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,127 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|Q15738|NSDHL_HUMAN,7.238605898123325,1.3404825737265416,4.557640750670242,5.361930294906166,5.093833780160858,6.434316353887399,2.680965147453083,5.898123324396782,5.361930294906166,9.115281501340483,2.680965147453083,5.093833780160858,6.166219839142091,4.557640750670242,5.093833780160858,4.289544235924933,6.166219839142091,8.310991957104557,0.5361930294906166,4.021447721179625,,50.670241286863266,32.707774798927616,49.59785522788203,9.919571045576408,13.136729222520106,9.651474530831099,15.013404825737265,21.983914209115284,9.651474530831099,10.455764075067023,,39,1,373 +sp|Q06830|PRDX1_HUMAN,6.030150753768844,2.0100502512562812,8.040201005025125,3.5175879396984926,7.537688442211055,8.040201005025125,2.0100502512562812,6.532663316582915,9.547738693467336,6.030150753768844,1.507537688442211,3.015075376884422,6.532663316582915,4.522613065326634,3.015075376884422,6.532663316582915,4.522613065326634,7.537688442211055,1.0050251256281406,2.512562814070352,,48.743718592964825,33.66834170854271,52.26130653266331,11.557788944723617,14.572864321608039,7.5376884422110555,12.56281407035176,21.608040201005025,11.055276381909547,11.055276381909549,,22,2,199 +sp|Q9Y371|SHLB1_HUMAN,8.493150684931507,1.36986301369863,4.931506849315069,7.9452054794520555,3.0136986301369864,5.205479452054795,1.095890410958904,4.931506849315069,6.8493150684931505,12.054794520547945,2.4657534246575343,6.027397260273973,3.287671232876712,4.931506849315069,4.931506849315069,7.397260273972603,7.123287671232877,4.10958904109589,0.547945205479452,3.287671232876712,,45.479452054794514,36.71232876712329,47.945205479452056,12.876712328767123,12.876712328767123,10.958904109589042,16.986301369863014,17.808219178082194,6.8493150684931505,14.520547945205479,,53,1,365 +sp|P08238|HS90B_HUMAN,5.248618784530387,0.8287292817679558,7.044198895027624,13.259668508287293,3.591160220994475,4.696132596685083,1.7955801104972375,6.629834254143646,10.359116022099448,8.56353591160221,2.6243093922651934,3.867403314917127,3.1767955801104977,2.9005524861878453,4.41988950276243,6.629834254143646,4.696132596685083,5.801104972375691,0.5524861878453038,3.314917127071823,,41.85082872928177,43.646408839779006,41.988950276243095,20.303867403314918,16.574585635359114,6.767955801104972,15.193370165745858,15.745856353591162,7.458563535911601,11.32596685082873,,82,7,724 +sp|O15530|PDPK1_HUMAN,5.935251798561151,1.618705035971223,5.0359712230215825,7.374100719424461,4.856115107913669,6.115107913669065,2.697841726618705,4.496402877697841,6.83453237410072,10.071942446043165,1.7985611510791366,3.237410071942446,6.83453237410072,5.0359712230215825,5.39568345323741,7.913669064748201,4.676258992805756,4.856115107913669,1.079136690647482,4.136690647482014,,44.96402877697841,35.61151079136691,46.22302158273381,12.410071942446043,14.928057553956835,8.273381294964029,14.568345323741006,16.906474820143885,10.071942446043165,12.589928057553957,,70,15,556 +sp|P22626|ROA2_HUMAN,3.1161473087818696,0.28328611898017,4.815864022662889,6.232294617563739,5.382436260623229,24.362606232294617,1.9830028328611897,2.5495750708215295,5.382436260623229,2.8328611898017,1.9830028328611897,5.382436260623229,4.2492917847025495,2.8328611898017,7.0821529745042495,7.0821529745042495,3.39943342776204,4.53257790368272,0.28328611898017,6.232294617563739,,51.55807365439094,33.711048158640224,57.22379603399433,11.048158640226628,14.44759206798867,8.215297450424929,5.38243626062323,32.01133144475921,11.898016997167138,10.48158640226629,,37,9,353 +sp|Q32P44|EMAL3_HUMAN,6.8080357142857135,2.1205357142857144,5.580357142857143,4.575892857142857,2.7901785714285716,12.834821428571427,2.7901785714285716,3.3482142857142856,3.125,9.151785714285714,1.0044642857142858,2.455357142857143,7.142857142857142,3.2366071428571432,6.584821428571429,10.9375,4.464285714285714,7.03125,1.7857142857142856,2.232142857142857,,49.10714285714285,28.348214285714285,59.37499999999999,10.15625,12.5,5.6919642857142865,12.5,26.67410714285714,6.808035714285715,15.401785714285715,,138,2,896 +sp|P41252|SYIC_HUMAN,4.992076069730586,1.8225039619651346,5.467511885895404,7.6069730586370845,4.595879556259905,5.229793977812995,1.7432646592709984,5.309033280507132,6.576862123613313,10.935023771790808,2.13946117274168,4.199683042789223,4.833597464342314,3.8034865293185423,5.071315372424722,5.705229793977813,6.259904912836767,8.003169572107765,1.5847860538827259,4.120443740095087,,48.73217115689383,34.46909667194929,46.513470681458,13.07448494453249,13.391442155309033,8.003169572107765,16.24405705229794,18.225039619651348,10.301109350237718,11.965134706814581,,151,1,1262 +sp|Q13283|G3BP1_HUMAN,4.721030042918455,0.2145922746781116,5.150214592274678,10.300429184549357,4.07725321888412,8.369098712446352,2.575107296137339,3.004291845493562,4.07725321888412,5.36480686695279,2.3605150214592276,4.506437768240343,10.515021459227468,6.437768240343347,7.939914163090128,5.793991416309012,3.004291845493562,9.44206008583691,0.2145922746781116,1.9313304721030045,,39.69957081545065,40.987124463519315,51.71673819742489,15.450643776824034,14.592274678111588,10.944206008583691,8.369098712446352,22.532188841201716,6.223175965665237,8.798283261802574,,41,4,466 +sp|P07900|HS90A_HUMAN,4.644808743169399,0.9562841530054645,7.377049180327869,13.25136612021858,3.415300546448088,4.371584699453552,1.639344262295082,6.830601092896176,10.92896174863388,8.469945355191257,2.73224043715847,4.2349726775956285,2.8688524590163933,3.415300546448088,4.098360655737705,5.737704918032787,5.8743169398907105,5.191256830601093,0.546448087431694,3.415300546448088,,40.57377049180328,44.94535519125684,41.256830601092894,20.62841530054645,16.666666666666664,7.650273224043716,15.300546448087433,14.207650273224045,7.3770491803278695,11.612021857923498,,85,6,732 +sp|Q9Y266|NUDC_HUMAN,5.438066465256798,0.3021148036253776,6.948640483383686,13.293051359516618,3.625377643504532,6.042296072507553,2.1148036253776437,3.625377643504532,10.27190332326284,8.761329305135952,3.625377643504532,4.229607250755287,3.0211480362537766,6.3444108761329305,6.042296072507553,5.740181268882175,4.229607250755287,4.229607250755287,1.2084592145015105,0.906344410876133,,37.764350453172206,49.24471299093656,40.181268882175225,20.241691842900302,18.429003021148038,10.574018126888218,12.386706948640484,15.709969788519636,5.740181268882176,9.969788519637461,,33,3,331 +sp|Q8NHW5|RLA0L_HUMAN,11.35646687697161,0.9463722397476341,5.047318611987381,6.624605678233439,4.73186119873817,6.624605678233439,1.2618296529968454,5.678233438485805,5.993690851735016,9.14826498422713,2.8391167192429023,4.73186119873817,5.3627760252365935,3.1545741324921135,3.7854889589905363,5.678233438485805,6.309148264984227,8.201892744479496,0.6309148264984227,1.8927444794952681,,52.05047318611988,30.599369085173503,54.25867507886436,11.67192429022082,11.041009463722398,7.886435331230284,14.826498422712934,26.182965299684547,7.2555205047318605,11.987381703470032,,38,2,317 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+sp|P22314|UBA1_HUMAN,7.655954631379962,1.7958412098298677,6.049149338374291,6.238185255198488,4.914933837429111,6.521739130434782,2.1739130434782608,3.780718336483932,5.00945179584121,10.113421550094518,2.2684310018903595,4.44234404536862,5.671077504725898,5.576559546313799,4.914933837429111,6.61625708884688,4.631379962192817,7.844990548204159,0.945179584120983,2.835538752362949,,48.67674858223063,34.40453686200379,51.22873345935728,12.28733459357278,12.098298676748582,10.01890359168242,13.89413988657845,22.022684310018903,8.695652173913043,11.247637051039696,,119,3,1058 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+sp|Q2KHR2|RFX7_HUMAN,5.722670579603815,1.247248716067498,4.108584005869406,4.91562729273661,2.641232575201761,5.282465150403522,2.641232575201761,3.9618488628026407,5.135730007336757,7.043286867204696,2.421129860601614,5.649303008070433,8.437270726338959,7.336757153338224,2.93470286133529,14.600146735143065,7.703595011005136,6.309611151870873,0.4402054292002935,1.467351430667645,,36.53705062362435,32.721936903888476,59.0608950843727,9.024211298606016,10.711665443873809,12.986060161408657,11.005135730007336,17.314746881878207,4.548789435069699,22.3037417461482,,304,2,1363 +sp|P26373|RL13_HUMAN,11.848341232227488,0.47393364928909953,1.8957345971563981,6.161137440758294,3.3175355450236967,4.265402843601896,1.8957345971563981,4.739336492890995,11.848341232227488,5.687203791469194,1.8957345971563981,3.3175355450236967,6.6350710900473935,3.3175355450236967,14.691943127962084,5.213270142180095,3.7914691943127963,6.6350710900473935,0.9478672985781991,1.4218009478672986,,41.232227488151665,43.127962085308056,44.07582938388626,8.056872037914692,28.436018957345972,6.6350710900473935,10.42654028436019,22.748815165876778,5.687203791469194,9.004739336492891,,19,2,211 +sp|P53396|ACLY_HUMAN,8.174386920980927,1.4532243415077202,5.358764759309718,5.722070844686648,3.9963669391462306,9.264305177111716,2.2706630336058127,6.993642143505904,6.539509536784741,8.174386920980927,3.088101725703906,3.178928247048138,5.267938237965486,2.997275204359673,4.35967302452316,5.540417801998183,5.722070844686648,7.266121707538602,0.9990917347865577,3.633060853769301,,53.042688465031794,30.42688465031789,51.22615803814713,11.080835603996366,13.169845594913713,6.176203451407811,15.16802906448683,24.704813805631247,8.628519527702089,11.262488646684831,,124,8,1101 +sp|Q71UI9|H2AV_HUMAN,14.0625,0.0,3.125,3.90625,0.78125,11.71875,4.6875,7.03125,10.9375,9.375,0.78125,0.78125,2.34375,3.90625,7.03125,6.25,6.25,5.46875,0.0,1.5625,,50.78125,34.375,50.0,7.03125,22.65625,4.6875,16.40625,31.25,2.34375,12.5,,16,1,128 +sp|P0C0S5|H2AZ_HUMAN,12.5,0.0,3.125,3.90625,0.78125,11.71875,4.6875,7.03125,10.9375,9.375,0.78125,0.78125,2.34375,3.90625,7.03125,7.03125,6.25,6.25,0.0,1.5625,,50.0,34.375,50.0,7.03125,22.65625,4.6875,16.40625,30.46875,2.34375,13.28125,,17,1,128 +sp|P06733|ENOA_HUMAN,9.90783410138249,1.3824884792626728,5.990783410138248,6.682027649769585,3.9170506912442393,8.755760368663594,1.3824884792626728,6.221198156682028,8.755760368663594,8.294930875576037,2.0737327188940093,5.529953917050691,3.686635944700461,2.5345622119815667,3.9170506912442393,5.990783410138248,4.147465437788019,7.603686635944701,0.6912442396313364,2.5345622119815667,,51.38248847926267,34.7926267281106,52.995391705069125,12.672811059907833,14.055299539170505,8.064516129032258,14.516129032258064,26.267281105990786,7.142857142857142,10.138248847926267,,44,3,434 +sp|P49368|TCPG_HUMAN,7.339449541284404,1.834862385321101,6.238532110091743,7.706422018348624,0.9174311926605505,6.605504587155964,1.651376146788991,9.541284403669724,6.605504587155964,8.440366972477065,4.036697247706423,3.486238532110092,3.302752293577982,4.587155963302752,6.422018348623854,5.871559633027523,6.238532110091743,6.7889908256880735,0.7339449541284404,1.651376146788991,,47.88990825688073,36.69724770642202,47.70642201834862,13.944954128440367,14.678899082568808,8.073394495412845,17.98165137614679,20.733944954128443,3.302752293577982,12.110091743119266,,66,2,545 +sp|Q9BTE3|MCMBP_HUMAN,4.984423676012461,2.336448598130841,5.451713395638629,6.853582554517133,3.894080996884735,4.205607476635514,2.959501557632399,3.894080996884735,4.8286604361370715,12.77258566978193,2.0249221183800623,5.763239875389408,6.386292834890965,5.451713395638629,4.672897196261682,7.320872274143301,5.14018691588785,6.697819314641744,1.2461059190031152,3.115264797507788,,45.17133956386292,35.98130841121495,48.28660436137071,12.305295950155763,12.461059190031154,11.214953271028037,16.666666666666664,15.88785046728972,8.255451713395638,12.46105919003115,,80,2,642 +sp|Q13126|MTAP_HUMAN,7.420494699646643,3.180212014134275,4.593639575971731,7.06713780918728,2.8268551236749118,7.06713780918728,3.180212014134275,7.773851590106007,6.36042402826855,7.420494699646643,3.180212014134275,2.8268551236749118,4.593639575971731,2.4734982332155475,4.946996466431095,6.007067137809187,9.187279151943462,6.713780918727916,1.4134275618374559,1.76678445229682,,48.76325088339223,31.448763250883392,51.590106007067135,11.660777385159012,14.48763250883392,5.30035335689046,15.194346289752652,21.20141342756184,6.007067137809187,15.19434628975265,,43,3,283 +sp|P50452|SPB8_HUMAN,7.754010695187167,2.6737967914438503,5.614973262032086,9.893048128342247,7.4866310160427805,4.545454545454546,1.8716577540106951,2.941176470588235,8.288770053475936,9.62566844919786,3.4759358288770055,4.010695187165775,2.941176470588235,2.6737967914438503,4.545454545454546,6.149732620320856,5.88235294117647,6.149732620320856,0.8021390374331552,2.6737967914438503,,48.12834224598931,36.89839572192514,45.721925133689844,15.508021390374333,14.705882352941178,6.684491978609626,12.566844919786096,18.44919786096257,10.962566844919786,12.032085561497325,,45,1,374 +sp|P35237|SPB6_HUMAN,6.648936170212766,1.5957446808510638,4.787234042553192,9.308510638297872,7.446808510638298,5.851063829787234,1.3297872340425532,3.4574468085106385,7.180851063829788,9.574468085106384,5.319148936170213,4.521276595744681,2.6595744680851063,3.4574468085106385,3.9893617021276597,7.446808510638298,6.117021276595745,6.382978723404255,0.7978723404255319,2.127659574468085,,49.20212765957447,34.57446808510638,46.01063829787234,14.095744680851062,12.500000000000002,7.9787234042553195,13.031914893617023,18.882978723404257,10.372340425531915,13.563829787234042,,51,1,376 +tr|A0A182DWH4|A0A182DWH4_HUMAN,4.511278195488721,1.8796992481203008,2.631578947368421,7.142857142857142,6.015037593984962,9.398496240601503,3.3834586466165413,1.1278195488721803,3.007518796992481,10.902255639097744,1.5037593984962405,3.3834586466165413,4.135338345864661,5.639097744360902,7.142857142857142,8.270676691729323,5.639097744360902,9.398496240601503,1.5037593984962405,3.3834586466165413,,49.62406015037594,32.330827067669176,49.24812030075188,9.774436090225564,13.533834586466165,9.022556390977444,12.030075187969924,23.308270676691727,10.902255639097744,13.909774436090224,,37,4,266
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/1R2 subs.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,119 @@ +Substrate,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,Phosphite +,,sp|Q15738|NSDHL_HUMAN, , , ,Q,A,T,S,xT,A,S,T,F,V,K,P, +,,sp|Q06830|PRDX1_HUMAN, , , , , ,N,S,xT,F,S,E,I,F,K, , +,,sp|Q9Y371|SHLB1_HUMAN, , , , , , ,S,xS,G,P,T,S,L,F,A, +,,sp|P08238|HS90B_HUMAN, , , , , , ,Q,xS,T,I,V,C,H,N,R, +,,sp|O15530|PDPK1_HUMAN, , , , , , ,A,xT,F,M,V,G,S,Y,G, +,,sp|P22626|ROA2_HUMAN, , , , , , , ,xS,T,F,A,A,F,F,T, +,,sp|Q32P44|EMAL3_HUMAN,N,S,T,M,L,G,A,xS,G,D,Y,A,D,F,Q, +,,sp|P41252|SYIC_HUMAN, , , , ,R,P,P,xS,A,F,F,L,F, , , +,,sp|Q13283|G3BP1_HUMAN,V,T,F,I,G,N,S,xT,A,I,Q,E,L,F,K, +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN, , , , , , , ,xS,P,G,S,Q,A,P,D, +,,sp|Q9Y266|NUDC_HUMAN, ,A,I,Q,G,G,T,xS,H,H,L,G,Q,N,F, +,,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN, , , , , ,V,H,xS,F,P,T,L,K, , , +,,sp|P22314|UBA1_HUMAN, , , , , ,A,G,xT,L,F,G,E,G,F,R, +,,sp|Q4KMQ1|TPRN_HUMAN, , , ,D,K,E,V,xS,D,D,E,A,E,E,K, +,,sp|O43760|SNG2_HUMAN, , , , , ,S,S,xT,P,L,P,T,I,S,S, +,,sp|Q9Y277|VDAC3_HUMAN, , , , , , , ,xS,P,E,G,E,Q,E,D, +,,sp|O75521|ECI2_HUMAN, , , , ,M,S,A,xT,F,I,G,N,S,T,A, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,S,P,T,G,P,S,N,xS,F,L,A,N,M,G,G, +,,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN, , , , , , ,G,xT,L,D,P,V,E,K, , +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN, , , , ,V,Y,A,xT,I,L,N,A,G,T,N, +,,sp|P07900|HS90A_HUMAN, , , , , ,V,C,xT,L,A,I,I,D,P,G, +,,sp|Q92499|DDX1_HUMAN, , , , , ,L,A,xT,F,W,Y,Y,A,K, , +,,sp|P63167|DYL1_HUMAN; sp|Q96FJ2|DYL2_HUMAN, , , , , ,T,G,xT,A,E,M,S,S,I,L, +,,sp|P24752|THIL_HUMAN, , , , ,Y,F,P,xT,Q,A,L,N,F,A,F, +,,sp|Q14161|GIT2_HUMAN, , , , , , ,D,xT,L,Y,E,A,V,R, , +,,sp|Q99832|TCPH_HUMAN, , , , , , ,Q,xT,L,M,W,S,A,T,W, +,,sp|A0FGR8|ESYT2_HUMAN, , , , , ,G,G,xT,I,L,A,P,T,V,S, +,,sp|Q15019|SEPT2_HUMAN, , , , ,I,Q,A,xS,T,M,A,F,K, , , +,,sp|Q15007|FL2D_HUMAN,S,A,T,F,I,G,N,xS,T,A,I,Q,E,L,F, +,,sp|O95218|ZRAB2_HUMAN, , , , , ,A,G,xT,F,I,A,P,P,V,Y, +,,sp|P22392|NDKB_HUMAN, , , , ,S,A,Q,xT,F,L,S,E,I,R, , +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN, , , , , , ,S,xS,F,S,H,Y,S,G,L, +,,sp|P00558|PGK1_HUMAN, , , , ,V,N,N,xS,T,M,L,G,A,S,G, +,,sp|Q14974|IMB1_HUMAN,Q,A,T,S,T,A,S,xT,F,V,K,P,I,F,S, +,,sp|Q8WUA2|PPIL4_HUMAN,C,A,N,P,A,A,G,xS,V,I,L,L,E,N,L, +,,sp|Q06830|PRDX1_HUMAN, , , ,T,G,Q,A,xT,V,A,S,G,I,P,A, +,,sp|P31323|KAP3_HUMAN, , , , , , ,T,xT,F,L,H,I,S,K, , +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN, , , , , ,Y,H,xT,I,N,G,H,N,C,E, +,,sp|P22626|ROA2_HUMAN, , , , ,I,S,S,xT,L,Y,Q,A,A,A,P, +,,sp|Q13263|TIF1B_HUMAN, , , , , , , ,xS,P,I,I,N,E,S,R, +,,sp|P67809|YBOX1_HUMAN, , , , ,T,F,T,xT,Q,E,T,I,T,N,A, +,,sp|P23193|TCEA1_HUMAN, , , , , , , ,xS,P,A,V,K,P,A,A, +,,sp|O15530|PDPK1_HUMAN, , , , , , , ,xS,P,T,T,V,L,F,T, +,,sp|P62995|TRA2B_HUMAN, , , , , , ,G,xS,F,T,L,L,W,P,S, +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN, , , , , ,G,Y,xS,F,S,L,T,T,F,S, +,,sp|P49915|GUAA_HUMAN, , , ,G,A,G,G,xT,I,I,T,N,F,E,R, +,,sp|Q16666|IF16_HUMAN, , , , , , ,I,xT,V,T,S,E,V,P,F, +,,sp|P11940|PABP1_HUMAN, , , , , ,S,R,xS,P,P,P,V,S,K, , +,,sp|P55884|EIF3B_HUMAN, , , ,S,S,G,P,xT,S,L,F,A,V,T,V, +,,sp|O15530|PDPK1_HUMAN, , ,A,S,F,N,D,xT,F,V,H,V,T,D,L, +,,sp|P50748|KNTC1_HUMAN, , , ,G,L,G,A,xT,F,I,L,R, , , , +,,sp|P26583|HMGB2_HUMAN;sp|P09429|HMGB1_HUMAN;, , , , , , ,A,xT,I,I,S,E,Q,Q,A, +,,sp|O95619|YETS4_HUMAN, , , ,A,A,V,P,xS,G,A,S,T,G,I,Y, +,,sp|P49321|NASP_HUMAN,E,A,E,A,A,H,G,xT,V,T,R, , , , , +,,sp|Q14C86|GAPD1_HUMAN, , , , , , ,S,xT,F,A,A,F,F,T,R, +,,sp|P47756|CAPZB_HUMAN, , , ,E,G,T,E,xT,F,A,D,H,R, , , +,,sp|Q7Z5L9|I2BP2_HUMAN, , , , , , ,Q,xT,P,S,F,W,I,L,A, +,,sp|P27824|CALX_HUMAN, , , ,V,G,A,F,xT,M,V,C,K, , , , +,,sp|P49407|ARRB1_HUMAN, , , , , ,F,E,xT,F,C,L,D,P,S,L, +,,sp|Q07020|RL18_HUMAN, , , , , ,T,G,xT,L,T,T,N,Q,M,S, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN, , , , ,G,L,A,xT,F,C,L,D,K, , , +,,sp|Q8IY67|RAVR1_HUMAN, ,A,N,S,F,V,G,xT,A,Q,Y,V,S,P,E, +,,sp|Q9UKW4|VAV3_HUMAN, ,G,G,Y,T,S,G,xT,F,R, , , , , , +,,sp|P00352|AL1A1_HUMAN, , , , , ,T,F,xT,T,Q,E,T,I,T,N, +,,sp|Q7KZF4|SND1_HUMAN, , , , , , ,K,xT,Q,T,V,C,N,F,T, +,,sp|P35244|RFA3_HUMAN, , , ,V,N,N,S,xT,M,L,G,A,S,G,D, +,,sp|P54886|P5CS_HUMAN,Q,N,T,S,R,P,P,xS,M,H,V,D,D,F,V, +,,tr|A0A096LPI6|A0A096LPI6_HUMAN; sp|P0DPI2|GAL3A_HUMAN; sp|A0A0B4J2D5|GAL3B_HUMAN,P,Q,G,E,E,E,E,xS,M,E,T,Q,E, , , +,,sp|Q16563|SYPL1_HUMAN, , , , , ,Y,P,xT,F,I,D,A,L,R, , +,,sp|E9PAV3|NACAM_HUMAN, , , ,Y,R,P,G,xT,V,A,L,R, , , , +,,sp|Q99547|MPH6_HUMAN, , , , , , ,G,xT,F,Y,Q,G,Y,R, , +,,sp|P49189|AL9A1_HUMAN, , , , , ,V,N,xT,L,I,R,P,D,G,E, +,,sp|P54819|KAD2_HUMAN, , , , ,A,L,D,xT,M,N,F,D,V,I,K, +,,sp|O00567|NOP56_HUMAN, , , , , , , ,xS,S,G,P,T,S,L,F, +,,sp|P62995|TRA2B_HUMAN, , , , , ,I,S,xS,T,L,Y,Q,A,A,A, +,,sp|O00541|PESC_HUMAN, , , , , , ,H,xT,L,T,Q,I,K, , , +,,sp|Q92900|RENT1_HUMAN, , , , , ,A,Y,xS,F,A,M,G,C,W,P, +,,sp|P40926|MDHM_HUMAN, , , , , , , ,xT,F,Y,N,Q,A,I,M, +,,tr|H7C0C1|H7C0C1_HUMAN; sp|P48047|ATPO_HUMAN, , , , , , ,S,xT,F,I,E,Y,F,G,K, +,,sp|P78527|PRKDC_HUMAN, , , ,V,A,V,A,xT,P,A,K, , , , , +,,sp|Q9Y3D7|TIM16_HUMAN, , , , , , , ,xS,P,S,V,S,S,P,E, +,,sp|Q9HC35|EMAL4_HUMAN, , , , , , ,G,xT,I,Q,V,I,T,Q,G, +,,sp|P29590|PML_HUMAN,T,G,Q,A,T,V,A,xS,G,I,P,A,G,W,M, +,,sp|P31943|HNRH1_HUMAN, , , , , , , ,xT,F,C,Q,L,I,L,D, +,,sp|Q01469|FABP5_HUMAN,I,T,A,L,A,P,S,xT,M,K, , , , , , +,,sp|P49321|NASP_HUMAN, , , , , ,A,P,xT,I,V,G,K, , , , +,,sp|Q02878|RL6_HUMAN,I,F,P,N,P,E,A,xT,F,V,K, , , , , +,,sp|P18124|RL7_HUMAN, , , , , ,T,F,xS,Y,A,G,F,E,M,Q, +,,sp|Q15942|ZYX_HUMAN, , , , , , , ,xT,F,T,T,Q,E,T,I, +,,sp|P30086|PEBP1_HUMAN, , , , , ,G,T,xT,I,T,L,V,L,K, , +,,sp|O43491|E41L2_HUMAN,G,A,S,Q,A,G,M,xT,G,Y,G,M,P,R, , +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN, , , , , , , ,xS,R,S,P,P,P,V,S, +,,sp|Q8ND56|LS14A_HUMAN, ,V,C,V,E,H,H,xT,F,Y,R, , , , , +,,sp|Q99873|ANM1_HUMAN, ,V,P,S,L,V,G,xS,F,I,R, , , , , +,,sp|P55265|DSRAD_HUMAN, , , , , , ,A,xT,L,W,Y,V,P,L,S, +,,sp|P53597|SUCA_HUMAN, , , , , ,S,P,xT,W,F,G,I,P,R, , +,,sp|O15530|PDPK1_HUMAN,L,L,Y,N,R,P,G,xT,V,S,S,L,K, , , +,,sp|C9JLW8|MCRI1_HUMAN, , ,S,S,G,P,T,xS,L,F,A,V,T,V,A, +,,sp|P25098|ARBK1_HUMAN,A,G,Y,D,P,T,P,xT,M,R, , , , , , +,,sp|Q86U90|YRDC_HUMAN, , , , , ,G,G,xT,M,V,T,Y,G,G,M, +,,sp|P52209|6PGD_HUMAN, , , , ,G,N,P,xT,V,E,V,D,L,F,T, +,,sp|Q9UQ35|SRRM2_HUMAN, , , , ,R,V,A,xT,P,V,D,W,K, , , +,,sp|Q6PI48|SYDM_HUMAN,A,G,G,P,R,P,E,xS,P,V,P,A,G,R, , +,,sp|P12956|XRCC6_HUMAN, , , , , , , ,xS,K,L,Q,I,H,R, , +,,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN, , , , ,G,Y,P,xT,L,L,W,F,R, , , +,,sp|Q9NZL9|MAT2B_HUMAN,G,A,P,G,Q,P,G,xT,I,L,R, , , , , +,,sp|Q2KHR2|RFX7_HUMAN, , , , , ,T,A,xT,I,T,E,P,R, , , +,,sp|P26373|RL13_HUMAN, , , , ,Q,A,T,xS,T,A,S,T,F,V,K, +,,sp|P53396|ACLY_HUMAN, , , , , , , ,xS,S,F,S,H,Y,S,G, +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN, , , ,E,R,S,P,xS,P,S,F,R, , , , +,,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN, , ,S,P,T,G,P,xS,N,S,F,L,A,N,M, +,,sp|P06733|ENOA_HUMAN,F,L,A,G,Y,D,P,xT,P,T,M,R, , , , +,,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN, , , , , ,S,T,xT,L,F,S,R, , , , +,,sp|P49368|TCPG_HUMAN, , , , , , , ,xT,G,T,L,T,T,N,Q, +,,sp|Q9BTE3|MCMBP_HUMAN, , , ,L,A,P,G,xT,I,V,E,V,W,K, , +,,sp|Q13126|MTAP_HUMAN, , ,A,I,Q,G,G,xT,S,H,H,L,G,Q,N, +,,sp|P50452|SPB8_HUMAN; sp|P35237|SPB6_HUMAN, ,V,C,N,Y,G,L,xT,F,T,Q,K, , , , +,,tr|A0A182DWH4|A0A182DWH4_HUMAN, , , , ,D,A,V,xT,Y,T,E,H,A,K, ,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/R1 SBF.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,88 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|P19338|NUCL_HUMAN,10.140845070422536,0.14084507042253522,10.28169014084507,14.507042253521126,3.6619718309859155,10.985915492957748,0.14084507042253522,2.3943661971830985,12.676056338028168,3.943661971830986,1.1267605633802817,2.9577464788732395,4.366197183098591,1.971830985915493,3.6619718309859155,5.070422535211268,5.352112676056338,5.211267605633803,0.28169014084507044,1.1267605633802817,,39.014084507042256,46.197183098591545,54.50704225352113,24.788732394366196,16.47887323943662,4.929577464788732,6.338028169014084,26.338028169014088,5.070422535211268,10.422535211267606,,74,13,710 +sp|P09651|ROA1_HUMAN,2.956989247311828,0.5376344086021506,4.838709677419355,4.838709677419355,6.182795698924731,25.0,2.1505376344086025,2.1505376344086025,4.838709677419355,2.1505376344086025,1.6129032258064515,5.64516129032258,2.6881720430107525,3.225806451612903,6.720430107526881,11.29032258064516,3.225806451612903,4.56989247311828,0.2688172043010753,5.10752688172043,,50.537634408602145,32.25806451612903,60.752688172043015,9.67741935483871,13.70967741935484,8.870967741935484,4.301075268817205,32.52688172043011,11.559139784946236,14.516129032258064,,54,6,372 +sp|Q32P51|RA1L2_HUMAN,3.4375000000000004,0.9375,5.625,5.3125,6.875000000000001,19.6875,2.5,2.5,5.9375,2.5,1.875,5.3125,3.125,3.4375000000000004,6.875000000000001,10.0,4.375,5.625,0.3125,3.75,,47.5,35.0,58.125,10.9375,15.3125,8.75,5.0,28.75,10.9375,14.375,,46,4,320 +sp|P22626|ROA2_HUMAN,3.1161473087818696,0.28328611898017,4.815864022662889,6.232294617563739,5.382436260623229,24.362606232294617,1.9830028328611897,2.5495750708215295,5.382436260623229,2.8328611898017,1.9830028328611897,5.382436260623229,4.2492917847025495,2.8328611898017,7.0821529745042495,7.0821529745042495,3.39943342776204,4.53257790368272,0.28328611898017,6.232294617563739,,51.55807365439094,33.711048158640224,57.22379603399433,11.048158640226628,14.44759206798867,8.215297450424929,5.38243626062323,32.01133144475921,11.898016997167138,10.48158640226629,,37,9,353 +sp|P60709|ACTB_HUMAN,7.733333333333333,1.6,6.133333333333333,6.933333333333333,3.4666666666666663,7.466666666666668,2.4,7.466666666666668,5.066666666666666,7.199999999999999,4.533333333333333,2.4,5.066666666666666,3.2,4.8,6.666666666666667,6.933333333333333,5.866666666666666,1.0666666666666667,4.0,,50.400000000000006,30.93333333333333,49.86666666666666,13.066666666666666,12.266666666666666,5.6,14.666666666666668,21.066666666666666,8.533333333333333,13.6,,51,15,375 +sp|P63261|ACTG_HUMAN,7.733333333333333,1.6,5.333333333333334,7.733333333333333,3.4666666666666663,7.466666666666668,2.4,7.733333333333333,5.066666666666666,7.199999999999999,4.533333333333333,2.4,5.066666666666666,3.2,4.8,6.666666666666667,6.933333333333333,5.6000000000000005,1.0666666666666667,4.0,,50.400000000000006,30.93333333333333,48.8,13.066666666666666,12.266666666666666,5.6,14.933333333333334,20.8,8.533333333333333,13.6,,51,15,375 +sp|P07195|LDHB_HUMAN,6.287425149700598,1.4970059880239521,5.688622754491018,6.287425149700598,1.4970059880239521,6.88622754491018,2.095808383233533,7.18562874251497,7.784431137724551,10.778443113772456,2.9940119760479043,5.089820359281437,3.293413173652695,3.293413173652695,2.3952095808383236,7.784431137724551,3.8922155688622757,11.377245508982035,1.7964071856287425,2.095808383233533,,52.395209580838326,32.634730538922156,51.796407185628745,11.976047904191617,12.275449101796408,8.383233532934131,17.964071856287426,24.550898203592816,5.389221556886227,11.676646706586826,,39,2,334 +sp|O75746|CMC1_HUMAN,9.587020648967552,1.0324483775811208,4.277286135693215,5.3097345132743365,6.1946902654867255,8.259587020648967,1.9174041297935103,5.752212389380531,5.014749262536873,10.176991150442479,1.4749262536873156,3.687315634218289,5.014749262536873,4.572271386430678,5.3097345132743365,5.752212389380531,5.162241887905605,7.227138643067847,0.5899705014749262,3.687315634218289,,53.98230088495574,30.08849557522124,50.0,9.587020648967552,12.24188790560472,8.259587020648967,15.92920353982301,25.073746312684364,10.47197640117994,10.914454277286136,,74,2,678 +sp|P42166|LAP2A_HUMAN,7.780979827089338,1.440922190201729,5.043227665706052,7.492795389048991,2.7377521613832854,6.195965417867435,1.8731988472622478,4.322766570605188,7.780979827089338,9.510086455331413,1.0086455331412103,3.170028818443804,6.340057636887608,5.043227665706052,4.899135446685879,11.815561959654179,6.051873198847262,5.3314121037463975,0.2881844380403458,1.8731988472622478,,40.48991354466858,35.30259365994236,53.170028818443804,12.536023054755043,14.553314121037465,8.213256484149856,13.8328530259366,19.308357348703172,4.899135446685879,17.86743515850144,,124,4,694 +sp|P11142|HSP7C_HUMAN,7.739938080495357,0.6191950464396285,7.120743034055728,7.5851393188854495,3.7151702786377707,8.204334365325078,1.08359133126935,6.811145510835913,8.359133126934983,6.811145510835913,2.0123839009287927,5.263157894736842,3.8699690402476783,4.024767801857585,4.3343653250774,5.41795665634675,7.275541795665634,7.120743034055728,0.30959752321981426,2.321981424148607,,45.6656346749226,37.77089783281734,52.63157894736842,14.705882352941178,13.777089783281733,9.287925696594428,13.622291021671826,23.065015479876163,6.346749226006192,12.693498452012385,,82,7,646 +sp|P0DMV8|HS71A_HUMAN,8.892355694227769,0.7800312012480499,7.020280811232449,7.332293291731669,3.9001560062402496,8.580343213728549,1.0920436817472698,6.5522620904836195,7.800312012480499,7.800312012480499,1.40405616224649,4.6801872074882995,3.74414976599064,4.212168486739469,4.83619344773791,5.30421216848674,6.3962558502340086,7.020280811232449,0.31201248049922,2.3400936037441498,,47.581903276131044,36.973478939157566,52.41809672386895,14.352574102964118,13.72854914196568,8.892355694227769,14.35257410296412,24.492979719188767,6.5522620904836195,11.700468018720748,,75,4,641 +sp|P0DMV9|HS71B_HUMAN,8.892355694227769,0.7800312012480499,7.020280811232449,7.332293291731669,3.9001560062402496,8.580343213728549,1.0920436817472698,6.5522620904836195,7.800312012480499,7.800312012480499,1.40405616224649,4.6801872074882995,3.74414976599064,4.212168486739469,4.83619344773791,5.30421216848674,6.3962558502340086,7.020280811232449,0.31201248049922,2.3400936037441498,,47.581903276131044,36.973478939157566,52.41809672386895,14.352574102964118,13.72854914196568,8.892355694227769,14.35257410296412,24.492979719188767,6.5522620904836195,11.700468018720748,,75,4,641 +sp|P49321|NASP_HUMAN,10.025380710659897,0.6345177664974619,5.32994923857868,19.416243654822335,1.015228426395939,7.233502538071066,0.7614213197969544,2.4111675126903553,7.868020304568528,6.598984771573605,1.6497461928934012,3.4263959390862944,4.187817258883249,4.568527918781726,2.284263959390863,7.868020304568528,4.822335025380711,8.248730964467004,0.25380710659898476,1.3959390862944163,,39.46700507614213,43.65482233502538,51.77664974619289,24.746192893401016,10.913705583756345,7.99492385786802,9.01015228426396,25.507614213197968,2.66497461928934,12.690355329949238,,100,4,788 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+sp|P14625|ENPL_HUMAN,5.47945205479452,0.62266500622665,8.094645080946451,13.20049813200498,3.8605230386052307,4.2341220423412205,1.2453300124533,5.1058530510585305,9.71357409713574,8.59277708592777,2.3661270236612704,3.4869240348692405,2.86425902864259,2.86425902864259,4.732254047322541,6.60024906600249,6.351183063511831,6.47571606475716,1.1207970112079702,2.9887920298879203,,40.84682440846824,43.33748443337485,44.20921544209215,21.29514321295143,15.69115815691158,6.351183063511831,13.6986301369863,16.1892901618929,7.970112079701121,12.951432129514322,,104,9,803 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+sp|P06748|NPM_HUMAN,6.462585034013606,1.0204081632653061,11.564625850340136,10.54421768707483,2.380952380952381,6.122448979591836,1.7006802721088436,3.4013605442176873,11.224489795918368,6.462585034013606,2.7210884353741496,3.061224489795918,5.782312925170068,4.421768707482993,2.7210884353741496,8.843537414965986,3.4013605442176873,6.122448979591836,0.6802721088435374,1.3605442176870748,,36.734693877551024,45.238095238095234,52.38095238095238,22.108843537414966,15.646258503401361,7.482993197278912,9.863945578231293,18.707482993197278,4.421768707482993,12.244897959183675,,36,7,294 +sp|P52272|HNRPM_HUMAN,8.082191780821917,0.684931506849315,3.4246575342465753,8.63013698630137,3.287671232876712,17.80821917808219,1.36986301369863,5.342465753424658,5.47945205479452,5.7534246575342465,8.63013698630137,4.2465753424657535,5.205479452054795,1.9178082191780823,7.397260273972603,4.383561643835616,1.9178082191780823,5.342465753424658,0.410958904109589,0.684931506849315,,56.02739726027397,32.465753424657535,51.09589041095891,12.054794520547945,14.246575342465754,6.164383561643836,11.095890410958905,31.232876712328764,4.383561643835616,6.301369863013699,,46,4,730 +sp|Q86VP6|CAND1_HUMAN,6.747967479674796,2.4390243902439024,6.666666666666667,6.016260162601626,2.8455284552845526,3.983739837398374,2.0325203252032518,6.260162601626017,6.341463414634147,13.658536585365855,2.5203252032520327,3.495934959349593,4.634146341463414,3.8211382113821135,4.146341463414634,9.024390243902438,5.365853658536586,7.235772357723577,0.24390243902439024,2.5203252032520327,,48.455284552845534,32.52032520325203,49.59349593495934,12.682926829268293,12.520325203252034,7.317073170731707,19.918699186991873,17.967479674796746,5.609756097560975,14.390243902439025,,177,2,1230 +sp|Q14697|GANAB_HUMAN,6.25,0.847457627118644,6.567796610169492,5.826271186440677,4.343220338983051,7.944915254237288,3.1779661016949152,3.6016949152542375,2.860169491525424,10.699152542372882,2.2245762711864407,2.9661016949152543,6.779661016949152,4.13135593220339,7.0974576271186445,6.779661016949152,4.661016949152542,6.885593220338983,2.5423728813559325,3.8135593220338984,,49.152542372881356,32.6271186440678,49.682203389830505,12.39406779661017,13.135593220338983,7.0974576271186445,14.30084745762712,21.08050847457627,10.699152542372882,11.440677966101696,,108,2,944 +sp|P51991|ROA3_HUMAN,2.1164021164021163,1.0582010582010581,5.291005291005291,5.82010582010582,5.026455026455026,27.24867724867725,1.8518518518518516,1.8518518518518516,5.555555555555555,2.1164021164021163,1.8518518518518516,4.497354497354497,3.968253968253968,3.1746031746031744,7.671957671957672,6.613756613756613,3.1746031746031744,5.026455026455026,0.26455026455026454,5.82010582010582,,52.38095238095238,33.86243386243386,58.994708994709,11.11111111111111,15.079365079365079,7.671957671957671,3.968253968253968,34.39153439153439,11.11111111111111,9.788359788359788,,37,2,378 +sp|P15880|RS2_HUMAN,8.532423208191126,1.7064846416382253,4.09556313993174,3.4129692832764507,3.754266211604096,14.675767918088736,1.3651877133105803,5.802047781569966,8.19112627986348,6.484641638225256,2.3890784982935154,1.3651877133105803,5.460750853242321,2.04778156996587,8.19112627986348,4.778156996587031,7.167235494880546,7.167235494880546,1.023890784982935,2.3890784982935154,,53.92491467576791,28.66894197952218,54.94880546075084,7.508532423208191,17.74744027303754,3.4129692832764507,12.286689419795222,30.37542662116041,7.167235494880546,11.945392491467576,,35,3,293 +sp|P07437|TBB5_HUMAN,6.756756756756757,1.8018018018018018,5.8558558558558556,8.108108108108109,5.18018018018018,7.882882882882883,2.2522522522522523,4.054054054054054,3.3783783783783785,7.207207207207207,3.8288288288288284,4.72972972972973,4.504504504504505,4.72972972972973,4.954954954954955,5.8558558558558556,6.981981981981981,7.4324324324324325,0.9009009009009009,3.6036036036036037,,48.648648648648646,34.00900900900901,51.80180180180181,13.963963963963964,10.585585585585585,9.45945945945946,11.26126126126126,22.07207207207207,9.684684684684685,12.837837837837837,,57,7,444 +sp|Q13509|TBB3_HUMAN,6.666666666666667,1.7777777777777777,5.777777777777778,8.222222222222223,4.888888888888889,7.555555555555555,2.4444444444444446,4.222222222222222,3.5555555555555554,7.333333333333333,4.222222222222222,4.666666666666667,4.444444444444445,4.666666666666667,4.888888888888889,7.111111111111111,6.0,6.888888888888889,0.8888888888888888,3.7777777777777777,,48.22222222222222,34.22222222222223,50.888888888888886,14.0,10.88888888888889,9.333333333333334,11.555555555555555,21.11111111111111,9.555555555555557,13.11111111111111,,59,4,450 +tr|A0A0B4J269|A0A0B4J269_HUMAN,8.281053952321205,3.0112923462986196,4.51693851944793,5.771643663739021,4.893350062735257,6.273525721455458,2.5094102885821834,4.893350062735257,3.0112923462986196,12.045169385194479,3.0112923462986196,3.7641154328732744,3.889585947302384,4.642409033877039,4.893350062735257,7.402760351317441,5.269761606022585,7.904642409033877,0.8782936010037641,3.136762860727729,,54.32873274780426,29.109159347553323,50.31367628607277,10.28858218318695,10.41405269761606,8.406524466750312,16.938519447929735,22.45922208281054,8.90840652446675,12.672521957340026,,101,4,797 +sp|Q9HCC0|MCCB_HUMAN,10.8348134991119,1.5985790408525755,5.150976909413854,5.683836589698046,4.085257548845471,10.124333925399645,1.9538188277087036,6.74955595026643,4.9733570159857905,8.170515097690942,2.1314387211367674,3.7300177619893424,4.7957371225577266,3.7300177619893424,6.039076376554174,5.150976909413854,3.5523978685612785,6.927175843694494,0.7104795737122558,3.9076376554174073,,55.23978685612789,31.26110124333925,51.86500888099467,10.8348134991119,12.966252220248668,7.460035523978685,14.920071047957371,27.88632326820604,8.703374777975133,8.703374777975133,,49,2,563 +sp|P30101|PDIA3_HUMAN,8.91089108910891,1.3861386138613863,6.732673267326733,8.514851485148515,5.742574257425743,6.138613861386139,1.782178217821782,4.752475247524752,9.504950495049505,8.118811881188119,1.5841584158415842,5.544554455445545,4.9504950495049505,1.782178217821782,4.554455445544554,5.742574257425743,4.158415841584159,5.742574257425743,0.594059405940594,3.762376237623762,,46.73267326732673,38.415841584158414,49.30693069306931,15.247524752475249,15.841584158415841,7.326732673267327,12.871287128712872,20.792079207920793,10.099009900990099,9.900990099009903,,50,2,505 +sp|P08865|RSSA_HUMAN,12.54237288135593,0.6779661016949152,5.084745762711865,8.47457627118644,3.389830508474576,5.084745762711865,1.3559322033898304,5.084745762711865,3.728813559322034,7.118644067796611,2.3728813559322033,3.050847457627119,6.779661016949152,5.084745762711865,5.084745762711865,4.745762711864407,8.135593220338983,6.440677966101695,3.389830508474576,2.3728813559322033,,48.474576271186436,31.864406779661017,52.54237288135594,13.559322033898304,10.16949152542373,8.135593220338984,12.203389830508476,24.06779661016949,9.152542372881356,12.88135593220339,,38,2,295 +sp|P62807|H2B1C_HUMAN,10.317460317460316,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873012,5.555555555555555,17.46031746031746,,22,2,126 +sp|O60814|H2B1K_HUMAN,11.11111111111111,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,10.317460317460316,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,41.26984126984127,37.3015873015873,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.809523809523807,5.555555555555555,16.666666666666664,,21,2,126 +sp|Q99880|H2B1L_HUMAN,10.317460317460316,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,4.761904761904762,2.380952380952381,4.761904761904762,15.873015873015872,5.555555555555555,2.380952380952381,2.380952380952381,3.968253968253968,2.380952380952381,6.349206349206349,11.904761904761903,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,49.2063492063492,7.936507936507937,24.6031746031746,4.761904761904762,10.317460317460316,22.22222222222222,5.555555555555555,18.253968253968253,,23,2,126 +sp|P58876|H2B1D_HUMAN,9.523809523809524,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,7.142857142857142,7.142857142857142,0.0,3.968253968253968,,39.68253968253968,37.3015873015873,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,22.22222222222222,5.555555555555555,18.253968253968253,,23,2,126 +sp|Q93079|H2B1H_HUMAN,10.317460317460316,0.0,3.1746031746031744,4.761904761904762,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,50.793650793650784,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873012,5.555555555555555,17.46031746031746,,22,2,126 +sp|Q5QNW6|H2B2F_HUMAN,9.523809523809524,0.0,3.1746031746031744,4.761904761904762,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,6.349206349206349,7.936507936507936,0.0,3.968253968253968,,40.476190476190474,37.3015873015873,50.79365079365079,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873016,5.555555555555555,17.46031746031746,,22,2,126 +sp|Q99877|H2B1N_HUMAN,9.523809523809524,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.873015873015872,4.761904761904762,2.380952380952381,2.380952380952381,4.761904761904762,2.380952380952381,6.349206349206349,11.904761904761903,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,39.68253968253968,37.3015873015873,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,22.22222222222222,5.555555555555555,18.253968253968253,,23,2,126 +sp|P57053|H2BFS_HUMAN,10.317460317460316,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,4.761904761904762,15.079365079365079,4.761904761904762,2.380952380952381,2.380952380952381,5.555555555555555,2.380952380952381,7.142857142857142,10.317460317460316,6.349206349206349,7.142857142857142,0.0,3.968253968253968,,40.476190476190474,37.301587301587304,50.0,7.936507936507937,24.6031746031746,4.761904761904762,9.523809523809524,23.015873015873012,5.555555555555555,16.666666666666664,,21,2,126 +sp|Q99879|H2B1M_HUMAN,8.73015873015873,0.0,2.380952380952381,5.555555555555555,1.5873015873015872,5.555555555555555,2.380952380952381,5.555555555555555,15.873015873015872,4.761904761904762,2.380952380952381,3.1746031746031744,4.761904761904762,2.380952380952381,6.349206349206349,11.11111111111111,5.555555555555555,7.936507936507936,0.0,3.968253968253968,,40.476190476190474,38.095238095238095,49.2063492063492,7.936507936507937,24.6031746031746,5.555555555555555,10.317460317460316,22.22222222222222,5.555555555555555,16.666666666666664,,21,2,126
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/R1 substrates.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,292 @@ + YSSPAPAD,sp|Q13283|G3BP1_HUMAN + TFYAWCNSHL,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN +DEEEDDDYEEDEEDD,sp|P19338|NUCL_HUMAN + VALAGYFHYYSCE,sp|Q15738|NSDHL_HUMAN + LAADAGYFLSR ,sp|Q9Y371|SHLB1_HUMAN +SHFEQWGYLTDCVVM,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN + YTIIGESI,sp|P54136|SYRC_HUMAN + GFGFVYFSSMAEV,sp|P22626|ROA2_HUMAN + GYPYLLLFR ,sp|Q8NBS9|TXND5_HUMAN + TVLSGGYTMYPGIA,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + SSYTFFELQE,sp|Q96JH7|VCIP1_HUMAN + SYSPAPADI,sp|Q13283|G3BP1_HUMAN + GLYSVINQK ,sp|P07195|LDHB_HUMAN + SYMVDPAIN,sp|Q15007|FL2D_HUMAN + AYFSEFAAK,sp|O14776|TCRG1_HUMAN +LCPTHADYLNNLANI,sp|O15294|OGT1_HUMAN + GIGYLHLKPTA,sp|Q9UKX7|NUP50_HUMAN + RPASYAGLPTTL,sp|O43312|MTSS1_HUMAN + LQYSSVLVSG,sp|P22314|UBA1_HUMAN + LAYATFAGIE,sp|O75746|CMC1_HUMAN + FFDHSGYLVMDAYE,sp|Q15005|SPCS2_HUMAN + RPHYPTPGIY ,sp|P62995|TRA2B_HUMAN + AVGTQYLSGAGLL,sp|Q13596|SNX1_HUMAN +SDEEREPYPVLGSGA,sp|P42166|LAP2A_HUMAN + VYFSSMAEV,sp|P22626|ROA2_HUMAN + IYITNDK ,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN + TYIFSPEGR,sp|P25789|PSA4_HUMAN + VNNAYLIGLGYT,sp|Q9Y277|VDAC3_HUMAN +PFSHLGQYPEGCSSY,sp|O75521|ECI2_HUMAN + ALYFSYGR ,sp|P04075|ALDOA_HUMAN + DKYPVREPID,sp|Q14498|RBM39_HUMAN + GPPDFSYDEEREPT,sp|P42166|LAP2A_HUMAN + ISGYFSSGWTV,sp|Q9UPN3|MACF1_HUMAN + YTLFVPR ,sp|P12955|PEPD_HUMAN + PEVNGGYGDAVPSG,sp|P49321|NASP_HUMAN + GCYIVKPFNL,sp|Q9ULW0|TPX2_HUMAN + STMVGYPYWMAPE,sp|Q13177|PAK2_HUMAN + EYTLHLVLR,sp|P62987|RL40_HUMAN; sp|P62979|RS27A_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; tr|A0A2R8Y422|A0A2R8Y422_HUMAN + TYYLVLDEA,sp|P17844|DDX5_HUMAN + TFNTYTGGLLLP,sp|P12956|XRCC6_HUMAN + LCPYHADSLNN,sp|O15294|OGT1_HUMAN +KLFIGGLYFETTDES,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN + YPPTTMLL,sp|Q9UGU5|HMGX4_HUMAN + GISCMNYTLSESPF,sp|Q15181|IPYR_HUMAN + VIYGTTLGYL,sp|Q9NUL3|STAU2_HUMAN + TPIGYFLGSLSL,sp|P24752|THIL_HUMAN + HIYIFSPEGR,sp|P60900|PSA6_HUMAN + LSHANYAVVLSAV,sp|P63010|AP2B1_HUMAN; sp|Q10567|AP1B1_HUMAN +GDGTTSVYLLAAEFL,sp|Q99832|TCPH_HUMAN + GSYFMDHVLR,sp|P53396|ACLY_HUMAN +GANTHLSYFSFTK ,sp|A0FGR8|ESYT2_HUMAN +ADDTVAPYSTFCK ,sp|P49407|ARRB1_HUMAN + YTMVDPAI,sp|Q15007|FL2D_HUMAN + SSTYFFELQES,sp|Q96JH7|VCIP1_HUMAN +AEVGDGTYSVTLLAA,sp|Q99832|TCPH_HUMAN + YPTGPSNS,sp|Q96I25|SPF45_HUMAN + GYAFVYFCTK ,sp|O60506|HNRPQ_HUMAN + LYLHGLQQY,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN +EVGDGTTYVTLLAAE,sp|Q99832|TCPH_HUMAN +AAVENLPYFLVELSR,sp|Q14974|IMB1_HUMAN + INEYFVDKDFV,sp|Q8WUA2|PPIL4_HUMAN +VARPEPAYGYTLEFR,sp|Q16658|FSCN1_HUMAN + AAYITATSPG,sp|P31323|KAP3_HUMAN +GDGTTTAYVLAR ,sp|P10809|CH60_HUMAN + VQAYLAANTFT,sp|P20290|BTF3_HUMAN + GCAFVYFSTR ,sp|O95319|CELF2_HUMAN + AEYFMFR ,sp|Q13126|MTAP_HUMAN +LINKPDGYFLLR ,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN + SYMVGTPYW,sp|Q13177|PAK2_HUMAN + LIAHAGYLLNLAK ,sp|Q9Y2X3|NOP58_HUMAN +FGFVTFSYMAEVDAA,sp|P22626|ROA2_HUMAN + ATVTPYPVKGK ,sp|Q9H1E3|NUCKS_HUMAN +AASAAAAYAASGSPG,sp|Q13263|TIF1B_HUMAN + SYIIGESIS,sp|P54136|SYRC_HUMAN + YFYNELR ,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + IYPYFLHLHGK,sp|Q08945|SSRP1_HUMAN + GYTFMDHVL,sp|P53396|ACLY_HUMAN +TQTVCNFYDGALVQH,sp|Q01469|FABP5_HUMAN + TGYTIAGVVY,sp|Q99436|PSB7_HUMAN + LGGYPTSLGTW,sp|P14314|GLU2B_HUMAN + YTIAGVVY,sp|Q99436|PSB7_HUMAN +KENQGDEYQGQQPPQ,sp|P67809|YBOX1_HUMAN + GLGYGTLYIAE,sp|P54105|ICLN_HUMAN +KPIGMGGYFIIQK ,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN; sp|Q9H0W9|CK054_HUMAN +DLINNLGYIAK ,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN +LQAYHTQYTPLIEYY,sp|P54819|KAD2_HUMAN + SADEPMYTFVVCNE,sp|P23193|TCEA1_HUMAN + YFHFNTVE,sp|P30740|ILEU_HUMAN + RPHTPYPGIYMGR,sp|P62995|TRA2B_HUMAN + SRPTYFADELAA,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN + LGGSPTYLGTWGSW,sp|P14314|GLU2B_HUMAN +PPTDVTPYFLTTGVL,sp|P49915|GUAA_HUMAN + TFNTSYGGLLLPS,sp|P12956|XRCC6_HUMAN +TVDDPYAYFVK ,sp|P23528|COF1_HUMAN + AYFYLLIGN,sp|O94826|TOM70_HUMAN + YYAICGAI,sp|P63220|RS21_HUMAN + KYVTAMDVV,sp|P62805|H4_HUMAN + PRPPYLLSQEQI,sp|P55884|EIF3B_HUMAN + RPAYTAGLPTT,sp|O43312|MTSS1_HUMAN + GYLLGESLK,sp|O75663|TIPRL_HUMAN + KPAYFMTSICD,sp|P53396|ACLY_HUMAN + GVYIVKPIVY,sp|O95619|YETS4_HUMAN +VVSGISAYSEDIPNK,sp|Q14C86|GAPD1_HUMAN + LSYLVETTLK,sp|P53041|PPP5_HUMAN +EAGDGTTYATVLAR ,sp|P10809|CH60_HUMAN +QVEHPSVYSPLTVEW,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN; + TVLYGGTTMYP,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + MYTGTFVVS,sp|P49189|AL9A1_HUMAN + GPPDFYSDEEREP,sp|P42166|LAP2A_HUMAN + DNHLLGYFDLTGIP,sp|P11021|BIP_HUMAN + ALYTMGFR ,sp|P30626|SORCN_HUMAN + RPAYVSSSAAV,sp|Q7Z5L9|I2BP2_HUMAN +SQSRPNSYALETLGG,sp|O94804|STK10_HUMAN + LQTSYVLVSGLR,sp|P22314|UBA1_HUMAN + AFGSYIVINPEK,sp|Q13620|CUL4B_HUMAN + TYPSYVAFT,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN +TCQVEHPYVTSPLTV,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN; +DTVAPSSYFCK ,sp|P49407|ARRB1_HUMAN + GCGYVLLSGPR,sp|Q07020|RL18_HUMAN + YLMNLGGL,sp|P37802|TAGL2_HUMAN +APSGPSGYLK ,sp|Q16658|FSCN1_HUMAN + LYFYAVSAP,sp|Q14156|EFR3A_HUMAN + YTELLIR ,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN + VTFYSMAEVDA,sp|P22626|ROA2_HUMAN + DSRPLYPILHIVK,sp|O95487|SC24B_HUMAN + LCYLFYTNEE,sp|P43243|MATR3_HUMAN + YPGSYFMDHVLR,sp|P53396|ACLY_HUMAN +SPGPSHPYFWTYTEA,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN; sp|Q6ZRS2|SRCAP_HUMAN + GYFVCIYSG,sp|Q96T68|SETB2_HUMAN + YTFYTALG,sp|Q9UIA9|XPO7_HUMAN +RPSTPGLYVVSGISA,sp|Q14C86|GAPD1_HUMAN + FSYFISEGVR,sp|P49848|TAF6_HUMAN +DIVLVGGYTR ,sp|P11142|HSP7C_HUMAN + ATFHYPFSHLGQ,sp|O75521|ECI2_HUMAN + GSTLYSPCQDFG,sp|P08567|PLEK_HUMAN +IPDDQKVYDDDKEKG,sp|Q86UE4|LYRIC_HUMAN + LQTYSVLVSGL,sp|P22314|UBA1_HUMAN + TVYAMDVVYA,sp|P62805|H4_HUMAN + VGYFFSEVK ,sp|P54886|P5CS_HUMAN + SRPYSFADELA,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN + LLAYTLVHSVK,sp|Q9NYF8|BCLF1_HUMAN + YLVNPANV,sp|O75608|LYPA1_HUMAN + GEPWYFLVR ,sp|P29350|PTN6_HUMAN + SPSSKPYLAVAVDS,sp|O60508|PRP17_HUMAN +DDTVAPSYTFCK ,sp|P49407|ARRB1_HUMAN +DAEVGDGYTSVTLLA,sp|Q99832|TCPH_HUMAN + AALYGLLHR ,sp|P55084|ECHB_HUMAN + RYEYLVGTIGK,sp|Q99547|MPH6_HUMAN + YYFAAHMDG,sp|Q15363|TMED2_HUMAN + YPGYTFMDHVL,sp|P53396|ACLY_HUMAN + LQAYHYQTTPLIE,sp|P54819|KAD2_HUMAN + YFNTSTGG,sp|P12956|XRCC6_HUMAN + IYFCTGIR ,sp|P55036|PSMD4_HUMAN + RPHYPTPGIYM,sp|P62995|TRA2B_HUMAN + GYVYLTPYR,sp|Q969T9|WBP2_HUMAN + SPHQLLYPSSFSPS,sp|Q14181|DPOA2_HUMAN + AYISNDGAT,sp|Q99832|TCPH_HUMAN + GVYQYYAYVT,sp|P26196|DDX6_HUMAN + ASQYRPNSSAL,sp|O94804|STK10_HUMAN + SEYPKEPEQL,sp|P09651|ROA1_HUMAN + YVWIAR ,sp|Q16629|SRSF7_HUMAN + LYLYDIAHT,sp|P40926|MDHM_HUMAN + LAYTILQHWK,sp|P78527|PRKDC_HUMAN + VTFSYMAEVDAA,sp|P22626|ROA2_HUMAN + GYFIEFR ,sp|Q92871|PMM1_HUMAN; sp|O15305|PMM2_HUMAN +IVLVGGSYR ,sp|P11142|HSP7C_HUMAN + YPHQLLSP,sp|Q14181|DPOA2_HUMAN +ASQSRPNYSALETLG,sp|O94804|STK10_HUMAN + YTYLVLDE,sp|P17844|DDX5_HUMAN + TCYFILR ,sp|Q99832|TCPH_HUMAN + QIFNGYFVK ,sp|P18124|RL7_HUMAN + GIYFIAAK ,tr|A0A1B0GU03|A0A1B0GU03_HUMAN; sp|P07339|CATD_HUMAN + SYLNEIYFG,sp|P47756|CAPZB_HUMAN + TGTYIAGVVYK,sp|Q99436|PSB7_HUMAN + SPYSKPSLAV,sp|O60508|PRP17_HUMAN + NRPTSIYWDGLDSG,sp|P30086|PEBP1_HUMAN + LYGVFAPR ,sp|P62701|RS4X_HUMAN; sp|Q8TD47|RS4Y2_HUMAN + SPYKAPHLQL,sp|O43491|E41L2_HUMAN + IGGIGYVPVGR ,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN + LYYLALHPNA,sp|P78527|PRKDC_HUMAN + VISGYTLGYLSP,sp|Q9NUL3|STAU2_HUMAN +AAAASAAYGSPGPGE,sp|Q13263|TIF1B_HUMAN + AYLYVTAIE,sp|Q99873|ANM1_HUMAN + TLPLYGSTFHDQ,sp|P55265|DSRAD_HUMAN + ACYILLR ,sp|P49368|TCPG_HUMAN +TPGLSVVYGISATSE,sp|Q14C86|GAPD1_HUMAN +IVLSGGSYMFR ,sp|P61158|ARP3_HUMAN + AFGYTIVINPE,sp|Q13620|CUL4B_HUMAN + ELYLLGKPK ,sp|Q00059|TFAM_HUMAN + PSSYPVIFAGG,sp|Q15366|PCBP2_HUMAN + ADYLWGIQK ,sp|P00338|LDHA_HUMAN + YIFQGIAA,sp|P52209|6PGD_HUMAN + RQNYFLVLR ,sp|Q6PI48|SYDM_HUMAN + QYYYLLNQAPD,sp|Q13283|G3BP1_HUMAN + AVGYQTLSGAG,sp|Q13596|SNX1_HUMAN + PSYSPVIFAG,sp|Q15366|PCBP2_HUMAN + LYYILGTTLK,sp|O75083|WDR1_HUMAN + AAYIVATSEG,sp|P13861|KAP2_HUMAN + AYIAGGGVI,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN + YLTLVDTG,sp|P08238|HS90B_HUMAN + GTVYFHSHSDH,sp|O75534|CSDE1_HUMAN + RPASVSYSAAVEHE,sp|Q7Z5L9|I2BP2_HUMAN + YFTAWCNS,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN + IGAYFLQR ,sp|P00505|AATM_HUMAN + SPYTLLPK ,sp|P27816|MAP4_HUMAN +GFGFVTFYSMAEVDA,sp|P22626|ROA2_HUMAN + LGYFLENR ,sp|Q09472|EP300_HUMAN + YTPSYVAF,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN + RYFNTSTGG,sp|P12956|XRCC6_HUMAN + NYTFTEHLY,sp|Q9BTE3|MCMBP_HUMAN + SGEVYYCQVEHPS,tr|A0A182DWH4|A0A182DWH4_HUMAN +TLPLTGSYFHDQIAM,sp|P55265|DSRAD_HUMAN + AMYPGYFYFQFK ,sp|Q9NRW3|ABC3C_HUMAN + FFDHYGTLVMDA,sp|Q15005|SPCS2_HUMAN + SYTTFFELQ,sp|Q96JH7|VCIP1_HUMAN + DKVNCYFYFK ,tr|M0R2N4|M0R2N4_HUMAN; sp|Q8WU68|U2AF4_HUMAN; sp|Q01081|U2AF1_HUMAN; sp|P0DN76|U2AF5_HUMAN +NIVLSGGYTMFR ,sp|P61158|ARP3_HUMAN + LYQTFLQLS,sp|Q92608|DOCK2_HUMAN + EYLVYLTHL,sp|O14980|XPO1_HUMAN + TGYFCALSTV,sp|P18433|PTPRA_HUMAN + DMYMFVTASK,sp|Q13347|EIF3I_HUMAN + ASYIFLSK ,sp|Q8ND76|CCNY_HUMAN; sp|Q8N7R7|CCYL1_HUMAN +GISCMNTYLSESPFK,sp|Q15181|IPYR_HUMAN + KTVYAMDVVYA,sp|P62805|H4_HUMAN +ADDKYNDYFWK ,sp|P14625|ENPL_HUMAN + ILYPIIFK ,sp|P82650|RT22_HUMAN + TPAYPVVHIR ,sp|P14866|HNRPL_HUMAN + ERDHSPYPSVFNSD,sp|Q6UN15|FIP1_HUMAN + LLYISGK ,sp|P06748|NPM_HUMAN + LGGSPYSLGTWGS,sp|P14314|GLU2B_HUMAN +VEHPSVTYPLTVEWR,sp|P01911|2B1F_HUMAN; sp|Q30154|DRB5_HUMAN +FGGSFAGYFGGAGGH,sp|P52272|HNRPM_HUMAN +VEHPSVTYPLTVEWS,tr|A0A182DWH4|A0A182DWH4_HUMAN +ATFHTPFYHLGQSPE,sp|O75521|ECI2_HUMAN + NSYFTEHLYR,sp|Q9BTE3|MCMBP_HUMAN + AVFPYIVGR ,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + LGYLSALDIL,sp|Q86VP6|CAND1_HUMAN + GMYLVTPLQL,sp|Q08211|DHX9_HUMAN + SSMYFLTR ,sp|Q9Y3I0|RTCB_HUMAN + YIFAYFTG,sp|Q9BRA2|TXD17_HUMAN + TFNYSTGGLLL,sp|P12956|XRCC6_HUMAN + LIFYTITSK ,sp|P43686|PRS6B_HUMAN +QAYHTQTYPLIEYYR,sp|P54819|KAD2_HUMAN + GQYLVVQFTV,sp|P27797|CALR_HUMAN + LYFQHDPET,sp|Q14697|GANAB_HUMAN + SPSYKPSLAVA,sp|O60508|PRP17_HUMAN + WGTLYDCVVMRD,sp|P51991|ROA3_HUMAN + ISVYFYHVK ,sp|P55884|EIF3B_HUMAN + YITAYTFAQAR ,sp|Q99575|POP1_HUMAN + GYGIVSAPV,sp|P15880|RS2_HUMAN + IGYIYGDLK ,sp|P49588|SYAC_HUMAN +RPASVSSYAAVEHEQ,sp|Q7Z5L9|I2BP2_HUMAN + YTIFSPEG,sp|P25789|PSA4_HUMAN + TYFYTALGR,sp|Q9UIA9|XPO7_HUMAN +GTGSGMGYLLISK ,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN + LYYILQGDSP,sp|O15042|SR140_HUMAN + GRLYPVPVPR ,sp|Q9UKM9|RALY_HUMAN + NTLFGYFHVAHSS,sp|Q13586|STIM1_HUMAN + YSTTFFEL,sp|Q96JH7|VCIP1_HUMAN + RPASVYSSAAVEH,sp|Q7Z5L9|I2BP2_HUMAN + DGYFVISK ,sp|Q8WUK0|PTPM1_HUMAN + SDGYFLVR ,sp|P15498|VAV_HUMAN + YHYVNGHNCE,sp|P09651|ROA1_HUMAN; tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN +LSVVSGIYATSEDIP,sp|Q14C86|GAPD1_HUMAN + QRSPYPAPAPAP,sp|Q9H7N4|SFR19_HUMAN + KQGYIFLAGPP,sp|Q9HCC0|MCCB_HUMAN + YNQAYPTFHQWR,sp|Q9UI08|EVL_HUMAN + SSYPAPADIA,sp|Q13283|G3BP1_HUMAN + YTMVGTPY,sp|Q13177|PAK2_HUMAN +QASLAANYFTITGHA,sp|P20290|BTF3_HUMAN + YTLNEIYF,sp|P47756|CAPZB_HUMAN + INQDGYFLVR ,sp|Q13094|LCP2_HUMAN + QRYPSPAPAP,sp|Q9H7N4|SFR19_HUMAN + YYIHSQLEH,sp|Q9BWJ5|SF3B5_HUMAN +YGVSGYPYLK ,sp|P30101|PDIA3_HUMAN + ERPVYMSFPLSS,sp|Q6ZNL6|FGD5_HUMAN + TLPLTGYTFHDQIA,sp|P55265|DSRAD_HUMAN + QIGYFASVEQF,sp|O60573|IF4E2_HUMAN + ARPAYAAVLVPL,sp|Q8WV74|NUDT8_HUMAN + GIYCMNTTLS,sp|Q15181|IPYR_HUMAN + AVFPYIVGRPR ,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + QGYQYTFSSI,sp|Q08945|SSRP1_HUMAN + AGYYFSNQAV,sp|Q14690|RRP5_HUMAN + YLTIVDTG,sp|P07900|HS90A_HUMAN + ETLVYLYHLDYVDT,sp|O14980|XPO1_HUMAN +HEEIAMAYVTALR ,sp|P04075|ALDOA_HUMAN + AYFHTPFSH,sp|O75521|ECI2_HUMAN +SADEPMTYFVVCNEC,sp|P23193|TCEA1_HUMAN +ASYVNLPYIALCNTD,sp|P08865|RSSA_HUMAN +TVLSGGTYMYPGIAD,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + ESYYVYVYK ,sp|P62807|H2B1C_HUMAN; sp|P57053|H2BFS_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P58876|H2B1D_HUMAN + LYFISGR ,sp|Q15005|SPCS2_HUMAN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/R2 SBf.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,127 @@ +Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of ST,Number of pST +sp|Q15738|NSDHL_HUMAN,7.238605898123325,1.3404825737265416,4.557640750670242,5.361930294906166,5.093833780160858,6.434316353887399,2.680965147453083,5.898123324396782,5.361930294906166,9.115281501340483,2.680965147453083,5.093833780160858,6.166219839142091,4.557640750670242,5.093833780160858,4.289544235924933,6.166219839142091,8.310991957104557,0.5361930294906166,4.021447721179625,,50.670241286863266,32.707774798927616,49.59785522788203,9.919571045576408,13.136729222520106,9.651474530831099,15.013404825737265,21.983914209115284,9.651474530831099,10.455764075067023,,39,1,373 +sp|Q06830|PRDX1_HUMAN,6.030150753768844,2.0100502512562812,8.040201005025125,3.5175879396984926,7.537688442211055,8.040201005025125,2.0100502512562812,6.532663316582915,9.547738693467336,6.030150753768844,1.507537688442211,3.015075376884422,6.532663316582915,4.522613065326634,3.015075376884422,6.532663316582915,4.522613065326634,7.537688442211055,1.0050251256281406,2.512562814070352,,48.743718592964825,33.66834170854271,52.26130653266331,11.557788944723617,14.572864321608039,7.5376884422110555,12.56281407035176,21.608040201005025,11.055276381909547,11.055276381909549,,22,2,199 +sp|Q9Y371|SHLB1_HUMAN,8.493150684931507,1.36986301369863,4.931506849315069,7.9452054794520555,3.0136986301369864,5.205479452054795,1.095890410958904,4.931506849315069,6.8493150684931505,12.054794520547945,2.4657534246575343,6.027397260273973,3.287671232876712,4.931506849315069,4.931506849315069,7.397260273972603,7.123287671232877,4.10958904109589,0.547945205479452,3.287671232876712,,45.479452054794514,36.71232876712329,47.945205479452056,12.876712328767123,12.876712328767123,10.958904109589042,16.986301369863014,17.808219178082194,6.8493150684931505,14.520547945205479,,53,1,365 +sp|P08238|HS90B_HUMAN,5.248618784530387,0.8287292817679558,7.044198895027624,13.259668508287293,3.591160220994475,4.696132596685083,1.7955801104972375,6.629834254143646,10.359116022099448,8.56353591160221,2.6243093922651934,3.867403314917127,3.1767955801104977,2.9005524861878453,4.41988950276243,6.629834254143646,4.696132596685083,5.801104972375691,0.5524861878453038,3.314917127071823,,41.85082872928177,43.646408839779006,41.988950276243095,20.303867403314918,16.574585635359114,6.767955801104972,15.193370165745858,15.745856353591162,7.458563535911601,11.32596685082873,,82,7,724 +sp|O15530|PDPK1_HUMAN,5.935251798561151,1.618705035971223,5.0359712230215825,7.374100719424461,4.856115107913669,6.115107913669065,2.697841726618705,4.496402877697841,6.83453237410072,10.071942446043165,1.7985611510791366,3.237410071942446,6.83453237410072,5.0359712230215825,5.39568345323741,7.913669064748201,4.676258992805756,4.856115107913669,1.079136690647482,4.136690647482014,,44.96402877697841,35.61151079136691,46.22302158273381,12.410071942446043,14.928057553956835,8.273381294964029,14.568345323741006,16.906474820143885,10.071942446043165,12.589928057553957,,70,15,556 +sp|P22626|ROA2_HUMAN,3.1161473087818696,0.28328611898017,4.815864022662889,6.232294617563739,5.382436260623229,24.362606232294617,1.9830028328611897,2.5495750708215295,5.382436260623229,2.8328611898017,1.9830028328611897,5.382436260623229,4.2492917847025495,2.8328611898017,7.0821529745042495,7.0821529745042495,3.39943342776204,4.53257790368272,0.28328611898017,6.232294617563739,,51.55807365439094,33.711048158640224,57.22379603399433,11.048158640226628,14.44759206798867,8.215297450424929,5.38243626062323,32.01133144475921,11.898016997167138,10.48158640226629,,37,9,353 +sp|Q32P44|EMAL3_HUMAN,6.8080357142857135,2.1205357142857144,5.580357142857143,4.575892857142857,2.7901785714285716,12.834821428571427,2.7901785714285716,3.3482142857142856,3.125,9.151785714285714,1.0044642857142858,2.455357142857143,7.142857142857142,3.2366071428571432,6.584821428571429,10.9375,4.464285714285714,7.03125,1.7857142857142856,2.232142857142857,,49.10714285714285,28.348214285714285,59.37499999999999,10.15625,12.5,5.6919642857142865,12.5,26.67410714285714,6.808035714285715,15.401785714285715,,138,2,896 +sp|P41252|SYIC_HUMAN,4.992076069730586,1.8225039619651346,5.467511885895404,7.6069730586370845,4.595879556259905,5.229793977812995,1.7432646592709984,5.309033280507132,6.576862123613313,10.935023771790808,2.13946117274168,4.199683042789223,4.833597464342314,3.8034865293185423,5.071315372424722,5.705229793977813,6.259904912836767,8.003169572107765,1.5847860538827259,4.120443740095087,,48.73217115689383,34.46909667194929,46.513470681458,13.07448494453249,13.391442155309033,8.003169572107765,16.24405705229794,18.225039619651348,10.301109350237718,11.965134706814581,,151,1,1262 +sp|Q13283|G3BP1_HUMAN,4.721030042918455,0.2145922746781116,5.150214592274678,10.300429184549357,4.07725321888412,8.369098712446352,2.575107296137339,3.004291845493562,4.07725321888412,5.36480686695279,2.3605150214592276,4.506437768240343,10.515021459227468,6.437768240343347,7.939914163090128,5.793991416309012,3.004291845493562,9.44206008583691,0.2145922746781116,1.9313304721030045,,39.69957081545065,40.987124463519315,51.71673819742489,15.450643776824034,14.592274678111588,10.944206008583691,8.369098712446352,22.532188841201716,6.223175965665237,8.798283261802574,,41,4,466 +sp|P07900|HS90A_HUMAN,4.644808743169399,0.9562841530054645,7.377049180327869,13.25136612021858,3.415300546448088,4.371584699453552,1.639344262295082,6.830601092896176,10.92896174863388,8.469945355191257,2.73224043715847,4.2349726775956285,2.8688524590163933,3.415300546448088,4.098360655737705,5.737704918032787,5.8743169398907105,5.191256830601093,0.546448087431694,3.415300546448088,,40.57377049180328,44.94535519125684,41.256830601092894,20.62841530054645,16.666666666666664,7.650273224043716,15.300546448087433,14.207650273224045,7.3770491803278695,11.612021857923498,,85,6,732 +sp|Q9Y266|NUDC_HUMAN,5.438066465256798,0.3021148036253776,6.948640483383686,13.293051359516618,3.625377643504532,6.042296072507553,2.1148036253776437,3.625377643504532,10.27190332326284,8.761329305135952,3.625377643504532,4.229607250755287,3.0211480362537766,6.3444108761329305,6.042296072507553,5.740181268882175,4.229607250755287,4.229607250755287,1.2084592145015105,0.906344410876133,,37.764350453172206,49.24471299093656,40.181268882175225,20.241691842900302,18.429003021148038,10.574018126888218,12.386706948640484,15.709969788519636,5.740181268882176,9.969788519637461,,33,3,331 +sp|Q8NHW5|RLA0L_HUMAN,11.35646687697161,0.9463722397476341,5.047318611987381,6.624605678233439,4.73186119873817,6.624605678233439,1.2618296529968454,5.678233438485805,5.993690851735016,9.14826498422713,2.8391167192429023,4.73186119873817,5.3627760252365935,3.1545741324921135,3.7854889589905363,5.678233438485805,6.309148264984227,8.201892744479496,0.6309148264984227,1.8927444794952681,,52.05047318611988,30.599369085173503,54.25867507886436,11.67192429022082,11.041009463722398,7.886435331230284,14.826498422712934,26.182965299684547,7.2555205047318605,11.987381703470032,,38,2,317 +sp|P05388|RLA0_HUMAN,11.987381703470032,0.9463722397476341,4.73186119873817,6.624605678233439,4.73186119873817,6.624605678233439,1.2618296529968454,6.309148264984227,5.993690851735016,9.14826498422713,2.8391167192429023,4.416403785488959,5.3627760252365935,3.1545741324921135,4.100946372239748,5.678233438485805,5.993690851735016,7.886435331230284,0.31545741324921134,1.8927444794952681,,52.6813880126183,30.283911671924294,53.62776025236593,11.35646687697161,11.35646687697161,7.570977917981073,15.457413249211356,26.498422712933756,6.940063091482649,11.67192429022082,,37,2,317 +sp|P22314|UBA1_HUMAN,7.655954631379962,1.7958412098298677,6.049149338374291,6.238185255198488,4.914933837429111,6.521739130434782,2.1739130434782608,3.780718336483932,5.00945179584121,10.113421550094518,2.2684310018903595,4.44234404536862,5.671077504725898,5.576559546313799,4.914933837429111,6.61625708884688,4.631379962192817,7.844990548204159,0.945179584120983,2.835538752362949,,48.67674858223063,34.40453686200379,51.22873345935728,12.28733459357278,12.098298676748582,10.01890359168242,13.89413988657845,22.022684310018903,8.695652173913043,11.247637051039696,,119,3,1058 +sp|Q4KMQ1|TPRN_HUMAN,12.517580872011253,0.7032348804500703,2.250351617440225,10.126582278481013,2.6722925457102673,8.438818565400844,1.2658227848101267,1.6877637130801686,3.6568213783403656,8.016877637130802,0.8438818565400843,1.6877637130801686,15.049226441631506,3.6568213783403656,8.579465541490858,9.142053445850914,3.2348804500703237,4.50070323488045,0.7032348804500703,1.2658227848101267,,41.35021097046413,31.223628691983123,57.52461322081575,12.376933895921239,13.50210970464135,5.344585091420534,9.70464135021097,25.457102672292546,4.641350210970464,12.376933895921237,,88,2,711 +sp|O43760|SNG2_HUMAN,12.053571428571429,2.232142857142857,5.357142857142857,2.6785714285714284,8.928571428571429,6.696428571428571,0.4464285714285714,3.571428571428571,2.232142857142857,7.142857142857142,0.8928571428571428,4.464285714285714,5.357142857142857,4.910714285714286,3.571428571428571,7.142857142857142,4.910714285714286,8.928571428571429,1.7857142857142856,6.696428571428571,,58.92857142857143,23.660714285714285,57.142857142857146,8.035714285714285,6.25,9.375,10.714285714285714,27.67857142857143,17.410714285714285,12.053571428571427,,27,1,224 +sp|Q9Y277|VDAC3_HUMAN,7.773851590106007,2.1201413427561837,4.946996466431095,3.8869257950530036,5.30035335689046,11.307420494699647,1.4134275618374559,3.8869257950530036,9.540636042402827,9.187279151943462,1.4134275618374559,6.713780918727916,1.4134275618374559,2.1201413427561837,1.4134275618374559,7.773851590106007,9.187279151943462,4.593639575971731,1.76678445229682,4.240282685512367,,51.590106007067135,30.035335689045937,55.830388692579504,8.833922261484098,12.367491166077738,8.8339222614841,13.074204946996467,23.674911660777386,11.307420494699647,16.96113074204947,,48,1,283 +sp|O75521|ECI2_HUMAN,8.883248730964468,1.7766497461928936,4.314720812182741,6.091370558375635,4.568527918781726,5.583756345177665,1.2690355329949239,3.807106598984772,8.375634517766498,9.390862944162437,2.7918781725888326,5.583756345177665,5.583756345177665,2.7918781725888326,4.568527918781726,8.121827411167512,5.83756345177665,7.1065989847715745,1.2690355329949239,2.284263959390863,,47.46192893401015,32.994923857868024,52.79187817258884,10.406091370558375,14.213197969543147,8.375634517766498,13.19796954314721,21.57360406091371,8.121827411167512,13.959390862944161,,55,4,394 +sp|Q5VTE0|EF1A3_HUMAN,8.441558441558442,1.2987012987012987,5.627705627705628,5.844155844155844,3.0303030303030303,9.523809523809524,2.1645021645021645,6.493506493506493,10.38961038961039,5.627705627705628,2.813852813852814,3.2467532467532463,5.411255411255411,2.1645021645021645,3.67965367965368,4.978354978354979,6.0606060606060606,9.523809523809524,1.0822510822510822,2.5974025974025974,,50.43290043290044,33.116883116883116,54.11255411255412,11.471861471861471,16.233766233766232,5.411255411255411,12.121212121212121,27.489177489177493,6.70995670995671,11.03896103896104,,51,7,462 +sp|P68104|EF1A1_HUMAN,8.441558441558442,1.2987012987012987,5.627705627705628,5.844155844155844,3.0303030303030303,9.523809523809524,2.1645021645021645,6.493506493506493,10.173160173160174,5.627705627705628,2.5974025974025974,3.463203463203463,5.411255411255411,2.1645021645021645,3.67965367965368,4.978354978354979,6.277056277056277,9.523809523809524,1.0822510822510822,2.5974025974025974,,50.21645021645023,33.116883116883116,54.54545454545455,11.471861471861471,16.017316017316016,5.627705627705628,12.121212121212121,27.489177489177493,6.70995670995671,11.255411255411255,,52,8,462 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+sp|P50452|SPB8_HUMAN,7.754010695187167,2.6737967914438503,5.614973262032086,9.893048128342247,7.4866310160427805,4.545454545454546,1.8716577540106951,2.941176470588235,8.288770053475936,9.62566844919786,3.4759358288770055,4.010695187165775,2.941176470588235,2.6737967914438503,4.545454545454546,6.149732620320856,5.88235294117647,6.149732620320856,0.8021390374331552,2.6737967914438503,,48.12834224598931,36.89839572192514,45.721925133689844,15.508021390374333,14.705882352941178,6.684491978609626,12.566844919786096,18.44919786096257,10.962566844919786,12.032085561497325,,45,1,374 +sp|P35237|SPB6_HUMAN,6.648936170212766,1.5957446808510638,4.787234042553192,9.308510638297872,7.446808510638298,5.851063829787234,1.3297872340425532,3.4574468085106385,7.180851063829788,9.574468085106384,5.319148936170213,4.521276595744681,2.6595744680851063,3.4574468085106385,3.9893617021276597,7.446808510638298,6.117021276595745,6.382978723404255,0.7978723404255319,2.127659574468085,,49.20212765957447,34.57446808510638,46.01063829787234,14.095744680851062,12.500000000000002,7.9787234042553195,13.031914893617023,18.882978723404257,10.372340425531915,13.563829787234042,,51,1,376 +tr|A0A182DWH4|A0A182DWH4_HUMAN,4.511278195488721,1.8796992481203008,2.631578947368421,7.142857142857142,6.015037593984962,9.398496240601503,3.3834586466165413,1.1278195488721803,3.007518796992481,10.902255639097744,1.5037593984962405,3.3834586466165413,4.135338345864661,5.639097744360902,7.142857142857142,8.270676691729323,5.639097744360902,9.398496240601503,1.5037593984962405,3.3834586466165413,,49.62406015037594,32.330827067669176,49.24812030075188,9.774436090225564,13.533834586466165,9.022556390977444,12.030075187969924,23.308270676691727,10.902255639097744,13.909774436090224,,37,4,266
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/R2 subs.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,118 @@ + QATSYASTFVKP,sp|Q15738|NSDHL_HUMAN + NSYFSEIFK ,sp|Q06830|PRDX1_HUMAN + SYGPTSLFA,sp|Q9Y371|SHLB1_HUMAN + QYTIVCHNR,sp|P08238|HS90B_HUMAN + AYFMVGSYG,sp|O15530|PDPK1_HUMAN + YTFAAFFT,sp|P22626|ROA2_HUMAN +NSTMLGAYGDYADFQ,sp|Q32P44|EMAL3_HUMAN + RPPYAFFLF ,sp|P41252|SYIC_HUMAN +VTFIGNSYAIQELFK,sp|Q13283|G3BP1_HUMAN + YPGSQAPD,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN + AIQGGTYHHLGQNF,sp|Q9Y266|NUDC_HUMAN + VHYFPTLK ,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN + AGYLFGEGFR,sp|P22314|UBA1_HUMAN + DKEVYDDEAEEK,sp|Q4KMQ1|TPRN_HUMAN + SSYPLPTISS,sp|O43760|SNG2_HUMAN + YPEGEQED,sp|Q9Y277|VDAC3_HUMAN + MSAYFIGNSTA,sp|O75521|ECI2_HUMAN +SPTGPSNYFLANMGG,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN + GYLDPVEK ,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN + VYAYILNAGTN,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN + VCYLAIIDPG,sp|P07900|HS90A_HUMAN + LAYFWYYAK ,sp|Q92499|DDX1_HUMAN + TGYAEMSSIL,sp|P63167|DYL1_HUMAN; sp|Q96FJ2|DYL2_HUMAN + YFPYQALNFAF,sp|P24752|THIL_HUMAN + DYLYEAVR ,sp|Q14161|GIT2_HUMAN + QYLMWSATW,sp|Q99832|TCPH_HUMAN + GGYILAPTVS,sp|A0FGR8|ESYT2_HUMAN + IQAYTMAFK ,sp|Q15019|SEPT2_HUMAN +SATFIGNYTAIQELF,sp|Q15007|FL2D_HUMAN + AGYFIAPPVY,sp|O95218|ZRAB2_HUMAN + SAQYFLSEIR ,sp|P22392|NDKB_HUMAN + SYFSHYSGL,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN + VNNYTMLGASG,sp|P00558|PGK1_HUMAN +QATSTASYFVKPIFS,sp|Q14974|IMB1_HUMAN +CANPAAGYVILLENL,sp|Q8WUA2|PPIL4_HUMAN + TGQAYVASGIPA,sp|Q06830|PRDX1_HUMAN + TYFLHISK ,sp|P31323|KAP3_HUMAN + YHYINGHNCE,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN + ISSYLYQAAAP,sp|P22626|ROA2_HUMAN + YPIINESR,sp|Q13263|TIF1B_HUMAN + TFTYQETITNA,sp|P67809|YBOX1_HUMAN + YPAVKPAA,sp|P23193|TCEA1_HUMAN + YPTTVLFT,sp|O15530|PDPK1_HUMAN + GYFTLLWPS,sp|P62995|TRA2B_HUMAN + GYYFSLTTFS,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN + GAGGYIITNFER,sp|P49915|GUAA_HUMAN + IYVTSEVPF,sp|Q16666|IF16_HUMAN + SRYPPPVSK ,sp|P11940|PABP1_HUMAN + SSGPYSLFAVTV,sp|P55884|EIF3B_HUMAN + ASFNDYFVHVTDL,sp|O15530|PDPK1_HUMAN + GLGAYFILR ,sp|P50748|KNTC1_HUMAN + AYIISEQQA,sp|P26583|HMGB2_HUMAN;sp|P09429|HMGB1_HUMAN; + AAVPYGASTGIY,sp|O95619|YETS4_HUMAN +EAEAAHGYVTR ,sp|P49321|NASP_HUMAN + SYFAAFFTR,sp|Q14C86|GAPD1_HUMAN + EGTEYFADHR ,sp|P47756|CAPZB_HUMAN + QYPSFWILA,sp|Q7Z5L9|I2BP2_HUMAN + VGAFYMVCK ,sp|P27824|CALX_HUMAN + FEYFCLDPSL,sp|P49407|ARRB1_HUMAN + TGYLTTNQMS,sp|Q07020|RL18_HUMAN + GLAYFCLDK ,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN + ANSFVGYAQYVSPE,sp|Q8IY67|RAVR1_HUMAN + GGYTSGYFR ,sp|Q9UKW4|VAV3_HUMAN + TFYTQETITN,sp|P00352|AL1A1_HUMAN + KYQTVCNFT,sp|Q7KZF4|SND1_HUMAN + VNNSYMLGASGD,sp|P35244|RFA3_HUMAN +QNTSRPPYMHVDDFV,sp|P54886|P5CS_HUMAN +PQGEEEEYMETQE ,tr|A0A096LPI6|A0A096LPI6_HUMAN; sp|P0DPI2|GAL3A_HUMAN; sp|A0A0B4J2D5|GAL3B_HUMAN + YPYFIDALR ,sp|Q16563|SYPL1_HUMAN + YRPGYVALR ,sp|E9PAV3|NACAM_HUMAN + GYFYQGYR ,sp|Q99547|MPH6_HUMAN + VNYLIRPDGE,sp|P49189|AL9A1_HUMAN + ALDYMNFDVIK,sp|P54819|KAD2_HUMAN + YSGPTSLF,sp|O00567|NOP56_HUMAN + ISYTLYQAAA,sp|P62995|TRA2B_HUMAN + HYLTQIK ,sp|O00541|PESC_HUMAN + AYYFAMGCWP,sp|Q92900|RENT1_HUMAN + YFYNQAIM,sp|P40926|MDHM_HUMAN + SYFIEYFGK,tr|H7C0C1|H7C0C1_HUMAN; sp|P48047|ATPO_HUMAN + VAVAYPAK ,sp|P78527|PRKDC_HUMAN + YPSVSSPE,sp|Q9Y3D7|TIM16_HUMAN + GYIQVITQG,sp|Q9HC35|EMAL4_HUMAN +TGQATVAYGIPAGWM,sp|P29590|PML_HUMAN + YFCQLILD,sp|P31943|HNRH1_HUMAN +ITALAPSYMK ,sp|Q01469|FABP5_HUMAN + APYIVGK ,sp|P49321|NASP_HUMAN +IFPNPEAYFVK ,sp|Q02878|RL6_HUMAN + TFYYAGFEMQ,sp|P18124|RL7_HUMAN + YFTTQETI,sp|Q15942|ZYX_HUMAN + GTYITLVLK ,sp|P30086|PEBP1_HUMAN +GASQAGMYGYGMPR ,sp|O43491|E41L2_HUMAN + YRSPPPVS,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN + VCVEHHYFYR ,sp|Q8ND56|LS14A_HUMAN + VPSLVGYFIR ,sp|Q99873|ANM1_HUMAN + AYLWYVPLS,sp|P55265|DSRAD_HUMAN + SPYWFGIPR ,sp|P53597|SUCA_HUMAN +LLYNRPGYVSSLK ,sp|O15530|PDPK1_HUMAN + SSGPTYLFAVTVA,sp|C9JLW8|MCRI1_HUMAN +AGYDPTPYMR ,sp|P25098|ARBK1_HUMAN + GGYMVTYGGM,sp|Q86U90|YRDC_HUMAN + GNPYVEVDLFT,sp|P52209|6PGD_HUMAN + RVAYPVDWK ,sp|Q9UQ35|SRRM2_HUMAN +AGGPRPEYPVPAGR ,sp|Q6PI48|SYDM_HUMAN + YKLQIHR ,sp|P12956|XRCC6_HUMAN + GYPYLLWFR ,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN +GAPGQPGYILR ,sp|Q9NZL9|MAT2B_HUMAN + TAYITEPR ,sp|Q2KHR2|RFX7_HUMAN + QATYTASTFVK,sp|P26373|RL13_HUMAN + YSFSHYSG,sp|P53396|ACLY_HUMAN + ERSPYPSFR ,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN + SPTGPYNSFLANM,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN +FLAGYDPYPTMR ,sp|P06733|ENOA_HUMAN + STYLFSR ,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN + YGTLTTNQ,sp|P49368|TCPG_HUMAN + LAPGYIVEVWK ,sp|Q9BTE3|MCMBP_HUMAN + AIQGGYSHHLGQN,sp|Q13126|MTAP_HUMAN + VCNYGLYFTQK ,sp|P50452|SPB8_HUMAN; sp|P35237|SPB6_HUMAN + DAVYYTEHAK ,tr|A0A182DWH4|A0A182DWH4_HUMAN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/S1.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,698 @@ +Substrates,Species,Reference,X.7,X.6,X.5,X.4,X.3,X.2,X.1,X0,X1,X2,X3,X4,X5,X6,X7,PhosphiteA,B +,,sp|Q13283|G3BP1_HUMAN,,,,,,,,xS,S,S,P,A,P,A,D,, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN,,,,,,T,F,xT,A,W,C,N,S,H,L,, +,,sp|P19338|NUCL_HUMAN,D,E,E,E,D,D,D,xS,E,E,D,E,E,D,D,, +,,sp|P19338|NUCL_HUMAN,,,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|Q15738|NSDHL_HUMAN,,,V,A,L,A,G,xT,F,H,Y,Y,S,C,E,, +,,sp|P13639|EF2_HUMAN,,,,,,T,G,xT,I,T,T,F,E,H,A,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,L,Y,A,N,T,V,L,xS,G,G,T,T,M,Y,P,, +,,sp|P11021|BIP_HUMAN,,,,,,,V,xT,H,A,V,V,T,V,P,, +,,sp|Q9HD20|AT131_HUMAN,,,,,,T,G,xT,L,T,S,D,S,L,V,, +,,sp|Q9UQB8|BAIP2_HUMAN,,,,Q,R,P,Y,xS,V,A,V,P,A,F,S,, +,,sp|Q9UQ35|SRRM2_HUMAN,T,S,T,Q,R,P,S,xS,P,E,T,A,T,K,,, +,,sp|Q06830|PRDX1_HUMAN,,,,,,,,xT,I,A,Q,D,Y,G,V,, +,,sp|Q9Y371|SHLB1_HUMAN,,L,A,A,D,A,G,xT,F,L,S,R,,,,, +,,sp|P08238|HS90B_HUMAN,,,I,E,D,V,G,xS,D,E,E,D,D,S,G,, +,,sp|Q14974|IMB1_HUMAN,,,,,,,T,xT,L,V,I,M,E,R,,, +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,S,H,F,E,Q,W,G,xT,L,T,D,C,V,V,M,, +,,sp|O15530|PDPK1_HUMAN,,,,,,,,xT,Y,Y,L,M,D,P,S,, +,,sp|Q14258|TRI25_HUMAN,,,,,,F,D,xT,I,Y,Q,I,L,L,K,, +,,sp|Q9Y5S9|RBM8A_HUMAN,,,,,,G,Y,xT,L,V,E,Y,E,T,Y,, +,,sp|P54136|SYRC_HUMAN,,,,,,,,xS,T,I,I,G,E,S,I,, +,,sp|P30086|PEBP1_HUMAN,,,G,N,D,I,S,xS,G,T,V,L,S,D,Y,, +,,sp|P22626|ROA2_HUMAN,,,G,F,G,F,V,xT,F,S,S,M,A,E,V,, +,,sp|P19338|NUCL_HUMAN,,A,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|Q32P44|EMAL3_HUMAN,,,,G,R,P,I,xT,M,Y,I,P,S,G,I,, +,,sp|Q8NBS9|TXND5_HUMAN,,,,,G,Y,P,xT,L,L,L,F,R,,,, +,,sp|P41252|SYIC_HUMAN,,,,,,T,G,xT,I,V,V,E,G,H,E,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,T,V,L,S,G,G,xT,T,M,Y,P,G,I,A,, +,,sp|Q96JH7|VCIP1_HUMAN,,,,,,S,S,xT,T,F,F,E,L,Q,E,, +,,sp|P09211|GSTP1_HUMAN,,,,,,,,xT,V,V,Y,F,P,V,R,, +,,sp|Q13283|G3BP1_HUMAN,,,,,,,S,xS,S,P,A,P,A,D,I,, +,,sp|P04083|ANXA1_HUMAN,S,A,V,S,P,Y,P,xT,F,N,P,S,S,D,V,, +,,sp|P07195|LDHB_HUMAN,,,,,,G,L,xT,S,V,I,N,Q,K,,, +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN,,,,,,S,L,xT,N,D,W,E,D,H,L,, +,,sp|P49321|NASP_HUMAN,G,S,G,D,A,V,P,xS,G,N,E,V,S,E,N,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN; sp|Q9BQE3|TBA1C_HUMAN,D,V,N,A,A,I,A,xT,I,K,,,,,,, +,,sp|P14625|ENPL_HUMAN,P,E,E,E,P,E,E,xT,A,E,D,T,T,E,D,, +,,sp|Q14554|PDIA5_HUMAN,,,,,G,Y,P,xT,F,H,Y,Y,H,Y,G,, +,,sp|Q15007|FL2D_HUMAN,,,,,,,S,xT,M,V,D,P,A,I,N,, +,,sp|Q9Y266|NUDC_HUMAN,,L,I,T,Q,T,F,xS,H,H,N,Q,L,A,Q,, +,,sp|P06748|NPM_HUMAN,,,,,,T,V,xS,L,G,A,G,A,K,,, +,,sp|O14776|TCRG1_HUMAN,,,,,,,A,xT,F,S,E,F,A,A,K,, +,,sp|O75534|CSDE1_HUMAN,,,,,,L,L,xT,S,Y,G,F,I,Q,C,, +,,sp|O15294|OGT1_HUMAN,L,C,P,T,H,A,D,xS,L,N,N,L,A,N,I,, +,,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN,,,,,,,,xT,S,F,F,Q,A,L,G,, +,,sp|Q9UKX7|NUP50_HUMAN,,,,,G,I,G,xT,L,H,L,K,P,T,A,, +,,sp|O43312|MTSS1_HUMAN,,,,R,P,A,S,xT,A,G,L,P,T,T,L,, +,,sp|Q00613|HSF1_HUMAN,D,T,E,G,R,P,P,xS,P,P,P,T,S,T,P,, +,,sp|P47712|PA24A_HUMAN,,,,,,Y,G,xT,F,M,A,P,D,L,F,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN; sp|Q9BQE3|TBA1C_HUMAN,T,I,G,G,G,D,D,xS,F,N,T,F,F,S,E,, +,,sp|P22314|UBA1_HUMAN,,,,,,L,Q,xT,S,S,V,L,V,S,G,, +,,sp|P53597|SUCA_HUMAN,,,,,,Q,G,xT,F,H,S,Q,Q,A,L,, +,,sp|O75746|CMC1_HUMAN,,,,,,L,A,xT,A,T,F,A,G,I,E,, +,,sp|Q96A26|F162A_HUMAN,,,,,,H,E,xT,L,T,S,L,N,L,E,, +,,sp|P51570|GALK1_HUMAN,I,Q,E,H,Y,G,G,xT,A,T,F,Y,L,S,Q,, +,,sp|Q15005|SPCS2_HUMAN,,F,F,D,H,S,G,xT,L,V,M,D,A,Y,E,, +,,sp|P30101|PDIA3_HUMAN,,,,,G,F,P,xT,I,Y,F,S,P,A,N,, +,,sp|P23193|TCEA1_HUMAN; sp|Q15560|TCEA2_HUMAN,,,,,T,G,G,xT,Q,T,D,L,F,T,C,, +,,sp|Q16851|UGPA_HUMAN,,,,,,I,Y,xT,F,N,Q,S,R,,,, +,,sp|P62995|TRA2B_HUMAN,,,,,R,P,H,xT,P,T,P,G,I,Y,,, +,,sp|Q13596|SNX1_HUMAN,,,A,V,G,T,Q,xT,L,S,G,A,G,L,L,, +,,sp|Q4KMQ1|TPRN_HUMAN,,,,W,Q,R,P,xS,S,P,P,P,F,L,P,, +,,sp|Q13200|PSMD2_HUMAN,,,,,,,G,xT,L,T,L,C,P,Y,H,, +,,sp|Q9UQ35|SRRM2_HUMAN,,,,,,,,xS,P,V,P,S,A,F,S,, +,,sp|P42166|LAP2A_HUMAN,S,D,E,E,R,E,P,xT,P,V,L,G,S,G,A,, +,,sp|O43776|SYNC_HUMAN,,,,K,E,D,G,xT,F,Y,E,F,G,E,D,, +,,sp|Q9HCC0|MCCB_HUMAN,,,,,,Q,G,xT,I,F,L,A,G,P,P,, +,,sp|P42166|LAP2A_HUMAN,,,,,,G,G,xT,L,F,G,G,E,V,C,, +,,sp|O43760|SNG2_HUMAN,,,,,A,G,G,xS,F,D,L,R,,,,, +,,sp|P30086|PEBP1_HUMAN,G,N,D,I,S,S,G,xT,V,L,S,D,Y,V,G,, +,,sp|P19338|NUCL_HUMAN,,,,V,A,V,A,xT,P,A,K,K,,,,, +,,sp|P22626|ROA2_HUMAN,,,,,,,V,xT,F,S,S,M,A,E,V,, +,,sp|P62701|RS4X_HUMAN; sp|Q8TD47|RS4Y2_HUMAN,,,,,,,L,xT,I,A,E,E,R,,,, +,,sp|Q6UN15|FIP1_HUMAN,,,,E,R,D,H,xS,P,T,P,S,V,F,N,, +,,sp|P40926|MDHM_HUMAN,,A,G,A,G,S,A,xT,L,S,M,A,Y,A,G,, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN,,,,,,,I,xT,I,T,N,D,K,,,, +,,sp|P00387|NB5R3_HUMAN,N,L,V,V,R,P,Y,xT,P,I,S,S,D,D,D,, +,,sp|P25789|PSA4_HUMAN,,,,,,,T,xT,I,F,S,P,E,G,R,, +,,sp|P07737|PROF1_HUMAN,,,,,,,S,xS,F,Y,V,N,G,L,T,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,,,S,P,H,xS,P,S,P,I,A,T,P,, +,,sp|P49189|AL9A1_HUMAN,,,,,V,I,A,xT,F,T,C,S,G,E,K,, +,,sp|P62942|FKB1A_HUMAN,,,,,R,G,Q,xT,C,V,V,H,Y,T,G,, +,,sp|P11021|BIP_HUMAN,,,,,,,I,xT,P,S,Y,V,A,F,T,, +,,sp|Q9Y277|VDAC3_HUMAN,,,,V,N,N,A,xS,L,I,G,L,G,Y,T,, +,,sp|O75521|ECI2_HUMAN,P,F,S,H,L,G,Q,xS,P,E,G,C,S,S,Y,, +,,sp|O60934|NBN_HUMAN,,,,,,Y,G,xT,F,V,N,E,E,K,,, +,,sp|P04075|ALDOA_HUMAN,,,,,,A,L,xT,F,S,Y,G,R,,,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,,,Q,xT,V,A,V,G,V,I,K,, +,,sp|P63244|RACK1_HUMAN,,,,,,D,K,xT,I,I,M,W,K,,,, +,,sp|Q92900|RENT1_HUMAN,,,,,T,V,T,xS,A,T,I,V,Y,H,L,, +,,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN,,,,,,,T,xT,I,I,W,D,A,H,T,, +,,sp|Q14498|RBM39_HUMAN,,,,,,D,K,xS,P,V,R,E,P,I,D,, +,,sp|P37198|NUP62_HUMAN,,,,E,Q,S,G,xT,I,Y,L,Q,H,A,D,, +,,sp|P42166|LAP2A_HUMAN,,G,P,P,D,F,S,xS,D,E,E,R,E,P,T,, +,,sp|Q9Y3L3|3BP1_HUMAN; sp|Q6ZT62|BGIN_HUMAN,,,,,,,,xS,P,P,E,T,A,A,P,, +,,sp|Q9UPN3|MACF1_HUMAN,,,,,I,S,G,xT,F,S,S,G,W,T,V,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,D,L,Y,A,N,xT,V,L,S,G,G,T,T,, +,,sp|P12955|PEPD_HUMAN,,,,,,,,xS,T,L,F,V,P,R,,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,,,E,I,xT,A,L,A,P,S,T,M,, +,,sp|P26641|EF1G_HUMAN,,,,,,,S,xT,F,V,L,D,E,F,K,, +,,sp|P49321|NASP_HUMAN,,P,E,V,N,G,G,xS,G,D,A,V,P,S,G,, +,,sp|Q92974|ARHG2_HUMAN,,,,E,R,P,S,xS,A,I,Y,P,S,D,S,, +,,sp|Q9ULW0|TPX2_HUMAN,,,,,,G,C,xT,I,V,K,P,F,N,L,, +,,sp|P49189|AL9A1_HUMAN,,,,,S,T,G,xT,F,V,V,S,Q,P,L,, +,,sp|P07900|HS90A_HUMAN,,,,,,T,L,xT,I,V,D,T,G,I,G,, +,,sp|Q9NP66|HM20A_HUMAN,,,,,,,,xS,P,L,T,G,Y,V,R,, +,,sp|Q13177|PAK2_HUMAN,,,S,T,M,V,G,xT,P,Y,W,M,A,P,E,, +,,sp|Q92841|DDX17_HUMAN,,,,,,,G,xT,A,Y,T,F,F,T,P,, +,,sp|Q7KZF4|SND1_HUMAN,,,,,,L,G,xT,L,S,P,A,F,S,T,, +,,sp|P62987|RL40_HUMAN; sp|P62979|RS27A_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG48|UBC_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; sp|P0CG47|UBB_HUMAN; tr|A0A2R8Y422|A0A2R8Y422_HUMAN,,,,,,,E,xS,T,L,H,L,V,L,R,, +,,sp|P09651|ROA1_HUMAN; sp|P51991|ROA3_HUMAN; sp|Q32P51|RA1L2_HUMAN,,,,,,W,G,xT,L,T,D,C,V,V,M,, +,,sp|P55263|ADK_HUMAN,,,,,,A,A,xT,F,F,G,C,I,G,I,, +,,sp|P17844|DDX5_HUMAN,,,,,,,T,xT,Y,L,V,L,D,E,A,, +,,sp|Q96FV9|THOC1_HUMAN,,,,,,S,N,xT,F,Y,S,A,G,K,,, +,,sp|Q92499|DDX1_HUMAN,N,T,R,P,G,A,N,xS,P,E,M,W,S,E,A,, +,,sp|Q01082|SPTB2_HUMAN,,,,,R,P,P,xS,P,E,P,S,T,K,,, +,,sp|P12956|XRCC6_HUMAN,,,,T,F,N,T,xS,T,G,G,L,L,L,P,, +,,sp|O15294|OGT1_HUMAN,,,,,L,C,P,xT,H,A,D,S,L,N,N,, +,,sp|P09651|ROA1_HUMAN; sp|Q32P51|RA1L2_HUMAN,K,L,F,I,G,G,L,xS,F,E,T,T,D,E,S,, +,,sp|Q9UQ35|SRRM2_HUMAN,A,P,F,S,E,P,G,xT,T,S,T,Q,R,P,S,, +,,sp|C9JLW8|MCRI1_HUMAN,,,S,P,P,S,S,xS,E,I,F,T,P,A,H,, +,,sp|P63167|DYL1_HUMAN; sp|Q96FJ2|DYL2_HUMAN,,,,,Y,N,P,xT,W,H,C,I,V,G,R,, +,,sp|Q9UGU5|HMGX4_HUMAN,,,,,,,,xS,P,P,T,T,M,L,L,, +,,sp|Q969T9|WBP2_HUMAN,,,,,,K,G,xT,V,Y,L,T,P,Y,R,, +,,sp|Q15181|IPYR_HUMAN,,G,I,S,C,M,N,xT,T,L,S,E,S,P,F,, +,,sp|P07195|LDHB_HUMAN,,,,,S,A,D,xT,L,W,D,I,Q,K,,, +,,sp|Q9Y678|COPG1_HUMAN,,,,,,,A,xT,F,Y,L,N,V,L,E,, +,,sp|P07437|TBB5_HUMAN,,,,,,,I,xS,V,Y,Y,N,E,A,T,, +,,sp|Q9NUL3|STAU2_HUMAN,,,,,,V,I,xS,G,T,T,L,G,Y,L,, +,,sp|P24752|THIL_HUMAN,,,,T,P,I,G,xS,F,L,G,S,L,S,L,, +,,sp|P60900|PSA6_HUMAN,,,,,,H,I,xT,I,F,S,P,E,G,R,, +,,sp|P63010|AP2B1_HUMAN; sp|Q10567|AP1B1_HUMAN,,,L,S,H,A,N,xS,A,V,V,L,S,A,V,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,E,I,T,A,L,A,P,xS,T,M,K,,,,,, +,,sp|P06748|NPM_HUMAN,A,V,E,E,D,A,E,xS,E,D,E,E,E,E,D,, +,,sp|Q14161|GIT2_HUMAN,,,,,,,G,xT,F,L,C,D,E,C,C,, +,,sp|Q15084|PDIA6_HUMAN,V,G,G,G,A,F,P,xT,I,V,E,R,,,,, +,,sp|P30086|PEBP1_HUMAN,,,,G,N,D,I,xS,S,G,T,V,L,S,D,, +,,sp|Q9UQ35|SRRM2_HUMAN,P,F,S,E,P,G,T,xT,S,T,Q,R,P,S,S,, +,,sp|Q92608|DOCK2_HUMAN,,,,,L,S,Q,xT,F,L,Q,L,S,D,G,, +,,sp|Q99832|TCPH_HUMAN,G,D,G,T,T,S,V,xT,L,L,A,A,E,F,L,, +,,sp|P53396|ACLY_HUMAN,,,,,,G,S,xT,F,M,D,H,V,L,R,, +,,sp|A0FGR8|ESYT2_HUMAN,G,A,N,T,H,L,S,xT,F,S,F,T,K,,,, +,,sp|Q15019|SEPT2_HUMAN,Y,H,L,P,D,A,E,xS,D,E,D,E,D,F,K,, +,,sp|Q15185|TEBP_HUMAN,,,,,,,L,xT,F,S,C,L,G,G,S,, +,,sp|P49407|ARRB1_HUMAN,A,D,D,T,V,A,P,xS,S,T,F,C,K,,,, +,,sp|Q15007|FL2D_HUMAN,,,,,,,,xS,T,M,V,D,P,A,I,, +,,sp|Q15370|ELOB_HUMAN,,,,,,,T,xT,I,F,T,D,A,K,,, +,,sp|Q96JH7|VCIP1_HUMAN,,,,,S,S,T,xT,F,F,E,L,Q,E,S,, +,,sp|Q99832|TCPH_HUMAN,A,E,V,G,D,G,T,xT,S,V,T,L,L,A,A,, +,,sp|O95218|ZRAB2_HUMAN,,E,V,E,D,K,E,xS,E,G,E,E,E,D,E,, +,,sp|P22392|NDKB_HUMAN,,,,,,,,xT,F,I,A,I,K,P,D,, +,,sp|O00461|GOLI4_HUMAN,L,E,H,N,A,E,E,xT,Y,G,E,N,D,E,N,, +,,sp|Q96I25|SPF45_HUMAN,,,,,,,,xS,P,T,G,P,S,N,S,, +,,sp|P10809|CH60_HUMAN,,,,,,,,xT,V,I,I,E,Q,S,W,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,,Y,V,xT,I,I,D,A,P,G,H,, +,,sp|O60506|HNRPQ_HUMAN,,,G,Y,A,F,V,xT,F,C,T,K,,,,, +,,sp|P04083|ANXA1_HUMAN,G,G,P,G,S,A,V,xS,P,Y,P,T,F,N,P,, +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN,,,,,,,L,xT,L,H,G,L,Q,Q,Y,, +,,sp|Q99832|TCPH_HUMAN,E,V,G,D,G,T,T,xS,V,T,L,L,A,A,E,, +,,sp|P00558|PGK1_HUMAN,Y,V,N,D,A,F,G,xT,A,H,R,,,,,, +,,sp|Q14974|IMB1_HUMAN,A,A,V,E,N,L,P,xT,F,L,V,E,L,S,R,, +,,sp|Q8WUA2|PPIL4_HUMAN,,,,,I,N,E,xT,F,V,D,K,D,F,V,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,N,T,V,L,S,G,G,xT,T,M,Y,P,G,I,A,, +,,sp|Q02878|RL6_HUMAN,,A,S,I,T,P,G,xT,I,L,I,I,L,T,G,, +,,sp|P46776|RL27A_HUMAN,,,,,,L,W,xT,L,V,S,E,Q,T,R,, +,,sp|P54105|ICLN_HUMAN,,,G,L,G,T,G,xT,L,Y,I,A,E,S,R,, +,,sp|Q06830|PRDX1_HUMAN,,,,,,,A,xT,A,V,M,P,D,G,Q,, +,,sp|Q16658|FSCN1_HUMAN,V,A,R,P,E,P,A,xT,G,Y,T,L,E,F,R,, +,,sp|P31323|KAP3_HUMAN,,,,,,A,A,xT,I,T,A,T,S,P,G,, +,,sp|P10809|CH60_HUMAN,G,D,G,T,T,T,A,xT,V,L,A,R,,,,, +,,sp|P20290|BTF3_HUMAN,,,,,V,Q,A,xS,L,A,A,N,T,F,T,, +,,sp|Q9UJ68|MSRA_HUMAN,,,,,E,G,Q,xT,F,Y,Y,A,E,D,Y,, +,,sp|P25705|ATPA_HUMAN,,,,,,,,xT,G,T,A,E,M,S,S,, +,,sp|Q16629|SRSF7_HUMAN,,,,,,A,F,xS,Y,Y,G,P,L,R,,, +,,sp|O95319|CELF2_HUMAN,,,G,C,A,F,V,xT,F,S,T,R,,,,, +,,sp|Q13126|MTAP_HUMAN,,,,,,A,E,xS,F,M,F,R,,,,, +,,sp|P17480|UBF1_HUMAN,,,,,R,P,V,xS,A,M,F,I,F,S,E,, +,,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN,L,I,N,K,P,D,G,xT,F,L,L,R,,,,, +,,sp|Q00610|CLH1_HUMAN,,,,,,A,H,xT,M,T,D,D,V,T,F,, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN,,,,,,R,V,xT,I,M,P,K,,,,, +,,sp|P49411|EFTU_HUMAN,,G,T,V,V,T,G,xT,L,E,R,,,,,, +,,sp|Q13177|PAK2_HUMAN,,,,,,,S,xT,M,V,G,T,P,Y,W,, +,,sp|Q10567|AP1B1_HUMAN,,,,G,L,E,I,xS,G,T,F,T,R,,,, +,,sp|Q9Y2X3|NOP58_HUMAN,,L,I,A,H,A,G,xS,L,L,N,L,A,K,,, +,,sp|P17844|DDX5_HUMAN,,,T,G,T,A,Y,xT,F,F,T,P,N,N,I,, +,,sp|P22626|ROA2_HUMAN,F,G,F,V,T,F,S,xS,M,A,E,V,D,A,A,, +,,sp|P11940|PABP1_HUMAN,,E,F,S,P,F,G,xT,I,T,S,A,K,,,, +,,sp|Q9H1E3|NUCKS_HUMAN,,,A,T,V,T,P,xS,P,V,K,,,,,, +,,sp|Q8TBC3|SHKB1_HUMAN,,,,,R,P,P,xT,P,A,P,W,P,S,S,, +,,sp|Q9H1E3|NUCKS_HUMAN,,,A,T,V,T,P,xS,P,V,K,G,K,,,, +,,sp|Q13263|TIF1B_HUMAN,A,A,S,A,A,A,A,xS,A,A,S,G,S,P,G,, +,,sp|P54136|SYRC_HUMAN,,,,,,,S,xT,I,I,G,E,S,I,S,, +,,sp|Q53H96|P5CR3_HUMAN,D,V,C,T,P,G,G,xT,T,I,Y,G,L,H,A,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,,,,,xT,F,Y,N,E,L,R,,, +,,sp|Q08945|SSRP1_HUMAN,,,,,I,Y,P,xT,F,L,H,L,H,G,K,, +,,sp|C9JLW8|MCRI1_HUMAN,,,,,S,P,P,xS,S,S,E,I,F,T,P,, +,,sp|P53396|ACLY_HUMAN,,,,,,,G,xS,T,F,M,D,H,V,L,, +,,sp|Q01469|FABP5_HUMAN,T,Q,T,V,C,N,F,xT,D,G,A,L,V,Q,H,, +,,sp|Q99436|PSB7_HUMAN,,,,,,T,G,xT,T,I,A,G,V,V,Y,, +,,sp|P14314|GLU2B_HUMAN,,,,,L,G,G,xS,P,T,S,L,G,T,W,, +,,sp|Q8N8J7|F241A_HUMAN,,,,,,M,G,xT,L,F,G,E,L,N,K,, +,,sp|Q92974|ARHG2_HUMAN,,,,,E,R,P,xS,S,A,I,Y,P,S,D,, +,,sp|P14625|ENPL_HUMAN,A,K,E,E,K,E,E,xS,D,D,E,A,A,V,E,, +,,sp|Q99436|PSB7_HUMAN,,,,,,,,xT,T,I,A,G,V,V,Y,, +,,sp|P67809|YBOX1_HUMAN,K,E,N,Q,G,D,E,xT,Q,G,Q,Q,P,P,Q,, +,,sp|P54105|ICLN_HUMAN,,,,,G,L,G,xT,G,T,L,Y,I,A,E,, +,,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN; sp|Q9H0W9|CK054_HUMAN,K,P,I,G,M,G,G,xT,F,I,I,Q,K,,,, +,,sp|P15880|RS2_HUMAN,,,,G,C,T,A,xT,L,G,N,F,A,K,,, +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN,D,L,I,N,N,L,G,xT,I,A,K,,,,,, +,,sp|P00338|LDHA_HUMAN,,,,,,,V,xT,L,T,S,E,E,E,A,, +,,sp|P54819|KAD2_HUMAN,L,Q,A,Y,H,T,Q,xT,T,P,L,I,E,Y,Y,, +,,sp|P23193|TCEA1_HUMAN,,S,A,D,E,P,M,xT,T,F,V,V,C,N,E,, +,,sp|P31943|HNRH1_HUMAN,,,Y,G,D,G,G,xS,T,F,Q,S,T,T,G,, +,,sp|O15530|PDPK1_HUMAN,,,,T,Q,T,E,xS,S,T,P,P,G,I,P,, +,,sp|P30740|ILEU_HUMAN,,,,,,,,xT,F,H,F,N,T,V,E,, +,,sp|P62995|TRA2B_HUMAN,,,R,P,H,T,P,xT,P,G,I,Y,M,G,R,, +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN,,,,S,R,P,T,xS,F,A,D,E,L,A,A,, +,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN,,,,,,Y,E,xS,L,T,D,P,S,K,,, +,,sp|P06733|ENOA_HUMAN,A,V,P,S,G,A,S,xT,G,I,Y,E,A,L,E,, +,,sp|P20042|IF2B_HUMAN,,,,,,,T,xS,F,V,N,F,T,D,I,, +,,sp|P54886|P5CS_HUMAN,,,,,,V,G,xT,F,F,S,E,V,K,P,, +,,sp|P14314|GLU2B_HUMAN,,L,G,G,S,P,T,xS,L,G,T,W,G,S,W,, +,,sp|P49915|GUAA_HUMAN,P,P,T,D,V,T,P,xT,F,L,T,T,G,V,L,, +,,sp|Q92541|RTF1_HUMAN,,,T,S,E,V,Y,xS,D,D,E,E,E,E,E,, +,,sp|Q9NSD9|SYFB_HUMAN,,,,,,T,Y,xT,I,A,N,Q,F,P,L,, +,,sp|Q16666|IF16_HUMAN,,,,,,,T,xT,I,Y,E,I,Q,D,D,, +,,sp|P12956|XRCC6_HUMAN,,,T,F,N,T,S,xT,G,G,L,L,L,P,S,, +,,sp|P23528|COF1_HUMAN,T,V,D,D,P,Y,A,xT,F,V,K,,,,,, +,,sp|Q13423|NNTM_HUMAN,,,,,,G,I,xT,H,I,G,Y,T,D,L,, +,,sp|P13639|EF2_HUMAN,,,,,,,,xS,T,L,T,D,S,L,V,, +,,sp|O94826|TOM70_HUMAN,,,,,,,A,xT,F,Y,L,L,I,G,N,, +,,sp|P63220|RS21_HUMAN,,,,,,,,xT,Y,A,I,C,G,A,I,, +,,sp|O15530|PDPK1_HUMAN,,,,P,G,A,G,xS,L,Q,H,A,Q,P,P,, +,,sp|P11940|PABP1_HUMAN,K,E,F,S,P,F,G,xT,I,T,S,A,K,,,, +,,sp|P62805|H4_HUMAN,,,,,,,K,xT,V,T,A,M,D,V,V,, +,,sp|Q9BT22|ALG1_HUMAN; sp|C9J202|AG1L2_HUMAN,,,,,,A,V,xT,V,Y,D,K,P,A,S,, +,,sp|O75746|CMC1_HUMAN,,,,L,A,T,A,xT,F,A,G,I,E,N,K,, +,,sp|P30086|PEBP1_HUMAN,,,,,N,R,P,xT,S,I,S,W,D,G,L,, +,,sp|P37198|NUP62_HUMAN,,,,,,E,Q,xS,G,T,I,Y,L,Q,H,, +,,sp|P55884|EIF3B_HUMAN,,,,P,R,P,P,xT,L,L,S,Q,E,Q,I,, +,,sp|O43312|MTSS1_HUMAN,,,,,R,P,A,xS,T,A,G,L,P,T,T,, +,,sp|O75663|TIPRL_HUMAN,,,,,,,G,xT,L,L,G,E,S,L,K,, +,,sp|P53396|ACLY_HUMAN,,,,,K,P,A,xS,F,M,T,S,I,C,D,, +,,sp|P47897|SYQ_HUMAN,,G,H,N,T,L,P,xS,P,W,R,,,,,, +,,sp|Q15366|PCBP2_HUMAN,Y,R,P,K,P,S,S,xS,P,V,I,F,A,G,G,, +,,sp|O15530|PDPK1_HUMAN,,,,,N,F,K,xT,F,F,V,H,T,P,N,, +,,sp|P50748|KNTC1_HUMAN,,,,,,L,T,xT,F,Y,G,A,F,G,P,, +,,sp|Q9UQ35|SRRM2_HUMAN,T,T,S,T,Q,R,P,xS,S,P,E,T,A,T,K,, +,,sp|P00558|PGK1_HUMAN,,,,,A,H,S,xS,M,V,G,V,N,L,P,, +,,sp|Q7Z5L9|I2BP2_HUMAN,,,,,R,K,P,xS,P,E,P,E,G,E,V,, +,,sp|P26583|HMGB2_HUMAN;sp|P09429|HMGB1_HUMAN;,,,,,R,P,P,xS,A,F,F,L,F,C,S,, +,,sp|O95619|YETS4_HUMAN,,,,,,G,V,xT,I,V,K,P,I,V,Y,, +,,sp|P49321|NASP_HUMAN,V,P,S,G,N,E,V,xS,E,N,M,E,E,E,A,, +,,sp|Q14C86|GAPD1_HUMAN,V,V,S,G,I,S,A,xT,S,E,D,I,P,N,K,, +,,sp|P53041|PPP5_HUMAN,,,,,,L,S,xT,L,V,E,T,T,L,K,, +,,sp|P22681|CBL_HUMAN,E,R,P,P,S,P,F,xS,M,A,P,Q,A,S,L,, +,,sp|P10809|CH60_HUMAN,E,A,G,D,G,T,T,xT,A,T,V,L,A,R,,, +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,Q,V,E,H,P,S,V,xT,S,P,L,T,V,E,W,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,,T,V,L,xS,G,G,T,T,M,Y,P,, +,,sp|P28066|PSA5_HUMAN,F,H,M,D,P,S,G,xT,F,V,Q,C,D,A,R,, +,,sp|P06748|NPM_HUMAN,E,A,M,N,Y,E,G,xS,P,I,K,,,,,, +,,sp|P22626|ROA2_HUMAN,,,,,,Y,H,xT,I,N,G,H,N,A,E,, +,,sp|Q16851|UGPA_HUMAN,,,,,,,G,xT,V,I,I,I,A,N,H,, +,,sp|Q5H9R7|PP6R3_HUMAN,,,,,,W,E,xT,F,C,T,S,S,L,G,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,Y,Y,V,xT,I,I,D,A,P,G,H,, +,,sp|P18031|PTN1_HUMAN,,,,Y,R,D,V,xS,P,F,D,H,S,R,,, +,,sp|P47756|CAPZB_HUMAN,,,,,,S,G,xS,G,T,M,N,L,G,G,, +,,sp|O15530|PDPK1_HUMAN,E,P,R,P,G,A,G,xS,L,Q,H,A,Q,P,P,, +,,sp|P49411|EFTU_HUMAN,,,,,,,T,xT,L,T,A,A,I,T,K,, +,,sp|P49189|AL9A1_HUMAN,,,,,,,M,xS,T,G,T,F,V,V,S,, +,,sp|P42166|LAP2A_HUMAN,,,G,P,P,D,F,xS,S,D,E,E,R,E,P,, +,,sp|P11021|BIP_HUMAN,,,,,I,T,P,xS,Y,V,A,F,T,P,E,, +,,sp|P11021|BIP_HUMAN,,D,N,H,L,L,G,xT,F,D,L,T,G,I,P,, +,,sp|P08236|BGLR_HUMAN,,,,S,L,D,P,xS,R,P,V,T,F,V,S,, +,,sp|P30626|SORCN_HUMAN,,,,,,A,L,xT,T,M,G,F,R,,,, +,,sp|Q7Z5L9|I2BP2_HUMAN,,,,,R,P,A,xS,V,S,S,S,A,A,V,, +,,sp|O94804|STK10_HUMAN,S,Q,S,R,P,N,S,xS,A,L,E,T,L,G,G,, +,,sp|P22314|UBA1_HUMAN,,,,L,Q,T,S,xS,V,L,V,S,G,L,R,, +,,sp|Q13620|CUL4B_HUMAN,,,,A,F,G,S,xT,I,V,I,N,P,E,K,, +,,sp|P27824|CALX_HUMAN,,,,,,,G,xT,L,S,G,W,I,L,S,, +,,sp|Q86YP4|P66A_HUMAN,,,,,R,P,P,xS,P,D,V,I,V,L,S,, +,,sp|O15530|PDPK1_HUMAN,,,,,,T,Q,xT,E,S,S,T,P,P,G,, +,,sp|E9PAV3|NACAM_HUMAN,,,S,P,A,S,D,xT,Y,I,V,F,G,E,A,, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN,,,,,,,T,xT,P,S,Y,V,A,F,T,, +,,sp|P51858|HDGF_HUMAN,A,G,D,L,L,E,D,xS,P,K,,,,,,, +,,sp|P01911|2B1F_HUMAN;sp|Q30154|DRB5_HUMAN;tr|A0A182DWH4|A0A182DWH4_HUMAN;,T,C,Q,V,E,H,P,xS,V,T,S,P,L,T,V,, +,,sp|O43252|PAPS1_HUMAN; sp|O95340|PAPS2_HUMAN,,,,,,G,C,xT,V,W,L,T,G,L,S,, +,,sp|P49407|ARRB1_HUMAN,D,T,V,A,P,S,S,xT,F,C,K,,,,,, +,,sp|Q07020|RL18_HUMAN,,,,,G,C,G,xT,V,L,L,S,G,P,R,, +,,sp|P37802|TAGL2_HUMAN,,,,,,,,xT,L,M,N,L,G,G,L,, +,,sp|Q16658|FSCN1_HUMAN,A,P,S,G,P,S,G,xT,L,K,,,,,,, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN,,,,,,,S,xT,C,I,Y,G,G,A,P,, +,,sp|Q14156|EFR3A_HUMAN,,,,,,,L,xT,F,Y,A,V,S,A,P,, +,,sp|P49189|AL9A1_HUMAN,,,,,,M,S,xT,G,T,F,V,V,S,Q,, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN,,,,,,,,xS,T,E,L,L,I,R,,, +,,sp|O00154|BACH_HUMAN,A,G,N,V,H,G,G,xT,I,L,K,,,,,, +,,sp|P22626|ROA2_HUMAN,,,,,V,T,F,xS,S,M,A,E,V,D,A,, +,,sp|O95487|SC24B_HUMAN,,,D,S,R,P,L,xS,P,I,L,H,I,V,K,, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN,,,,,,,,xS,T,C,I,Y,G,G,A,, +,,sp|Q8IY67|RAVR1_HUMAN,L,S,A,V,H,S,P,xT,F,C,Q,L,A,C,G,, +,,sp|Q68EM7|RHG17_HUMAN,,,,,R,P,A,xS,M,A,V,M,E,G,D,, +,,sp|Q9Y266|NUDC_HUMAN,,,,L,I,T,Q,xT,F,S,H,H,N,Q,L,, +,,sp|P43243|MATR3_HUMAN,,,,,,L,C,xS,L,F,Y,T,N,E,E,, +,,sp|P08567|PLEK_HUMAN,,,,,,G,S,xT,L,T,S,P,C,Q,D,, +,,sp|Q9UKW4|VAV3_HUMAN,,,,,,,G,xT,F,Y,Q,G,Y,L,C,, +,,sp|P53396|ACLY_HUMAN,,,,Y,P,G,S,xT,F,M,D,H,V,L,R,, +,,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN; sp|Q6ZRS2|SRCAP_HUMAN,S,P,G,P,S,H,P,xT,F,W,T,Y,T,E,A,, +,,sp|Q96T68|SETB2_HUMAN,,,,,,,G,xT,F,V,C,I,Y,S,G,, +,,sp|P21439|MDR3_HUMAN; sp|P08183|MDR1_HUMAN,,,,,,,T,xT,I,V,I,A,H,R,,, +,,sp|Q9UIA9|XPO7_HUMAN,,,,,,,,xT,T,F,Y,T,A,L,G,, +,,sp|Q14C86|GAPD1_HUMAN,R,P,S,T,P,G,L,xS,V,V,S,G,I,S,A,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,S,P,H,S,P,xS,P,I,A,T,P,P,S,, +,,sp|P49848|TAF6_HUMAN,,,,,,F,S,xT,F,I,S,E,G,V,R,, +,,sp|P11142|HSP7C_HUMAN,D,I,V,L,V,G,G,xS,T,R,,,,,,, +,,sp|O75521|ECI2_HUMAN,,,,A,T,F,H,xT,P,F,S,H,L,G,Q,, +,,sp|P08567|PLEK_HUMAN,,,,G,S,T,L,xT,S,P,C,Q,D,F,G,, +,,sp|P00352|AL1A1_HUMAN,,,,,A,N,N,xT,F,Y,G,L,S,A,G,, +,,sp|Q9Y266|NUDC_HUMAN,,,,,,L,I,xT,Q,T,F,S,H,H,N,, +,,sp|Q86UE4|LYRIC_HUMAN,I,P,D,D,Q,K,V,xS,D,D,D,K,E,K,G,, +,,sp|P19338|NUCL_HUMAN,,,,,,,V,xT,L,D,W,A,K,P,K,, +,,sp|Q53H96|P5CR3_HUMAN,V,C,T,P,G,G,T,xT,I,Y,G,L,H,A,L,, +,,sp|P52701|MSH6_HUMAN,,,,,,,Q,xS,T,L,Y,S,F,F,P,, +,,sp|P22314|UBA1_HUMAN,,,,,L,Q,T,xS,S,V,L,V,S,G,L,, +,,sp|Q7KZF4|SND1_HUMAN,V,D,Y,I,R,P,A,xS,P,A,T,E,T,V,P,, +,,sp|P62805|H4_HUMAN,,,,,,T,V,xT,A,M,D,V,V,Y,A,, +,,sp|Q5TC12|ATPF1_HUMAN,,,A,Q,S,C,P,xT,F,L,C,A,L,P,R,, +,,sp|P35244|RFA3_HUMAN,,,,,,,A,xT,I,L,C,T,S,Y,V,, +,,sp|P54886|P5CS_HUMAN,,,,,,V,G,xT,F,F,S,E,V,K,,, +,,sp|Q9Y4E1|WAC2C_HUMAN; sp|Q641Q2|WAC2A_HUMAN,,,,,S,R,P,xT,S,F,A,D,E,L,A,, +,,sp|Q96C86|DCPS_HUMAN,,,,,,,T,xT,V,V,Y,P,A,T,E,, +,,tr|A0A096LPI6|A0A096LPI6_HUMAN; sp|P0DPI2|GAL3A_HUMAN; sp|A0A0B4J2D5|GAL3B_HUMAN,,,,,,N,L,xS,T,F,A,V,D,G,K,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,,,L,L,A,xS,T,L,V,H,S,V,K,, +,,sp|O75608|LYPA1_HUMAN,,,,,,,,xT,L,V,N,P,A,N,V,, +,,sp|P29350|PTN6_HUMAN,,,,G,E,P,W,xT,F,L,V,R,,,,, +,,sp|Q16563|SYPL1_HUMAN,,,,,,T,V,xT,A,T,F,G,Y,P,F,, +,,sp|E9PAV3|NACAM_HUMAN,,,,,S,P,A,xS,D,T,Y,I,V,F,G,, +,,sp|Q16851|UGPA_HUMAN,,,,,,G,G,xT,L,T,Q,Y,E,G,K,, +,,sp|O60508|PRP17_HUMAN,,S,P,S,S,K,P,xS,L,A,V,A,V,D,S,, +,,sp|P49407|ARRB1_HUMAN,D,D,T,V,A,P,S,xS,T,F,C,K,,,,, +,,sp|Q99832|TCPH_HUMAN,D,A,E,V,G,D,G,xT,T,S,V,T,L,L,A,, +,,sp|P78371|TCPB_HUMAN,,,,,,L,T,xS,F,I,G,A,I,A,I,, +,,sp|P16150|LEUK_HUMAN,,,R,P,T,L,T,xT,F,F,G,R,,,,, +,,sp|P55084|ECHB_HUMAN,,,,,A,A,L,xT,G,L,L,H,R,,,, +,,sp|P45880|VDAC2_HUMAN,,,,,,,L,xT,F,D,T,T,F,S,P,, +,,sp|P60174|TPIS_HUMAN,,,,D,C,G,A,xT,W,V,V,L,G,H,S,, +,,sp|Q99547|MPH6_HUMAN,,,,,R,Y,E,xT,L,V,G,T,I,G,K,, +,,sp|P08236|BGLR_HUMAN,L,D,P,S,R,P,V,xT,F,V,S,N,S,N,Y,, +,,sp|Q15363|TMED2_HUMAN,,,,,,,Y,xT,F,A,A,H,M,D,G,, +,,sp|P53396|ACLY_HUMAN,,,,,Y,P,G,xS,T,F,M,D,H,V,L,, +,,sp|P47756|CAPZB_HUMAN,,,,S,G,S,G,xT,M,N,L,G,G,S,L,, +,,sp|P49189|AL9A1_HUMAN,,,,M,S,T,G,xT,F,V,V,S,Q,P,L,, +,,sp|P54819|KAD2_HUMAN,,,L,Q,A,Y,H,xT,Q,T,T,P,L,I,E,, +,,sp|O00567|NOP56_HUMAN,,L,I,A,H,A,G,xS,L,T,N,L,A,K,,, +,,sp|P12956|XRCC6_HUMAN,,,,,,,,xT,F,N,T,S,T,G,G,, +,,sp|P55036|PSMD4_HUMAN,,,,,,,I,xT,F,C,T,G,I,R,,, +,,sp|P62995|TRA2B_HUMAN,,,,,R,P,H,xT,P,T,P,G,I,Y,M,, +,,sp|Q9UQ35|SRRM2_HUMAN,Q,S,H,S,G,S,I,xS,P,Y,P,K,,,,, +,,sp|Q969T9|WBP2_HUMAN,,,,,,,G,xT,V,Y,L,T,P,Y,R,, +,,sp|P11142|HSP7C_HUMAN,,,,,D,A,G,xT,I,A,G,L,N,V,L,, +,,sp|P11021|BIP_HUMAN,,,,,D,A,G,xT,I,A,G,L,N,V,M,, +,,sp|O00541|PESC_HUMAN,,,,E,R,Y,P,xT,F,I,D,A,L,R,,, +,,sp|P08238|HS90B_HUMAN,,,,,,T,L,xT,L,V,D,T,G,I,G,, +,,sp|Q14181|DPOA2_HUMAN,,S,P,H,Q,L,L,xS,P,S,S,F,S,P,S,, +,,sp|P35249|RFC4_HUMAN,,,,,,A,I,xT,F,L,Q,S,A,T,R,, +,,sp|P19338|NUCL_HUMAN,,,,K,V,V,V,xS,P,T,K,K,,,,, +,,sp|Q99832|TCPH_HUMAN,,,,,,,A,xT,I,S,N,D,G,A,T,, +,,sp|Q53H96|P5CR3_HUMAN,,,,S,D,V,C,xT,P,G,G,T,T,I,Y,, +,,sp|P62081|RS7_HUMAN,,,,,,V,E,xT,F,S,G,V,Y,K,,, +,,sp|Q92900|RENT1_HUMAN,,,T,V,T,S,A,xT,I,V,Y,H,L,A,R,, +,,sp|P26196|DDX6_HUMAN,,,,,,G,V,xT,Q,Y,Y,A,Y,V,T,, +,,sp|O94804|STK10_HUMAN,,,,,A,S,Q,xS,R,P,N,S,S,A,L,, +,,sp|P05455|LA_HUMAN,,,,,,,,xS,P,S,K,P,L,P,E,, +,,sp|P09651|ROA1_HUMAN,,,,,,S,E,xS,P,K,E,P,E,Q,L,, +,,sp|Q92900|RENT1_HUMAN,,,,,,T,V,xT,S,A,T,I,V,Y,H,, +,,sp|Q16629|SRSF7_HUMAN,,,,,,,,xT,V,W,I,A,R,,,, +,,sp|P40926|MDHM_HUMAN,,,,,,,L,xT,L,Y,D,I,A,H,T,, +,,tr|H7C0C1|H7C0C1_HUMAN; sp|P48047|ATPO_HUMAN,,,,,,Y,A,xT,A,L,Y,S,A,A,S,, +,,sp|P26373|RL13_HUMAN,,,,,,L,A,xT,Q,L,T,G,P,V,M,, +,,sp|P78527|PRKDC_HUMAN,,,,,,L,A,xT,T,I,L,Q,H,W,K,, +,,sp|Q9Y3D7|TIM16_HUMAN,,,,S,V,G,G,xS,F,Y,L,Q,S,K,,, +,,sp|P00338|LDHA_HUMAN,,,,,S,A,D,xT,L,W,G,I,Q,K,,, +,,sp|P55884|EIF3B_HUMAN,,,,,,,V,xT,L,M,Q,L,P,T,R,, +,,sp|Q16658|FSCN1_HUMAN,Y,L,A,P,S,G,P,xS,G,T,L,K,,,,, +,,sp|Q9HC35|EMAL4_HUMAN,,,,G,R,P,I,xT,M,F,I,P,S,D,V,, +,,sp|P22626|ROA2_HUMAN,,,,V,T,F,S,xS,M,A,E,V,D,A,A,, +,,sp|Q92871|PMM1_HUMAN; sp|O15305|PMM2_HUMAN,,,,,,,G,xT,F,I,E,F,R,,,, +,,sp|P29590|PML_HUMAN,,,,,,T,P,xT,L,T,S,I,Y,C,R,, +,,sp|P31943|HNRH1_HUMAN,,Y,G,D,G,G,S,xT,F,Q,S,T,T,G,H,, +,,sp|P07737|PROF1_HUMAN,,S,T,G,G,A,P,xT,F,N,V,T,V,T,K,, +,,sp|P11142|HSP7C_HUMAN,I,V,L,V,G,G,S,xT,R,,,,,,,, +,,sp|P62191|PRS4_HUMAN,,A,V,A,N,Q,T,xS,A,T,F,L,R,,,, +,,sp|Q01469|FABP5_HUMAN,,,,,,,T,xT,Q,F,S,C,T,L,G,, +,,sp|Q14181|DPOA2_HUMAN,,,,,,,,xS,P,H,Q,L,L,S,P,, +,,sp|O94804|STK10_HUMAN,A,S,Q,S,R,P,N,xS,S,A,L,E,T,L,G,, +,,sp|P49321|NASP_HUMAN,E,P,E,V,N,G,G,xS,G,D,A,V,P,S,G,, +,,sp|P17844|DDX5_HUMAN,,,,,,,,xT,T,Y,L,V,L,D,E,, +,,sp|Q99832|TCPH_HUMAN,,,,,,T,C,xT,F,I,L,R,,,,, +,,sp|Q02878|RL6_HUMAN,,,,,V,L,A,xT,V,T,K,P,V,G,G,, +,,sp|P18124|RL7_HUMAN,,,Q,I,F,N,G,xT,F,V,K,,,,,, +,,tr|A0A1B0GU03|A0A1B0GU03_HUMAN; sp|P07339|CATD_HUMAN,,,,,,G,I,xT,F,I,A,A,K,,,, +,,sp|Q8IVH4|MMAA_HUMAN,,,,,,,,xS,T,F,I,E,Y,F,G,, +,,sp|Q15942|ZYX_HUMAN,,,,,,,,xS,P,G,A,P,G,P,L,, +,,sp|Q01469|FABP5_HUMAN,,,,,,T,Q,xT,V,C,N,F,T,D,G,, +,,sp|P11021|BIP_HUMAN,,V,T,H,A,V,V,xT,V,P,A,Y,F,N,D,, +,,sp|O15530|PDPK1_HUMAN,Q,G,P,A,M,D,G,xT,A,A,E,P,R,P,G,, +,,sp|Q9H0L4|CSTFT_HUMAN; sp|P33240|CSTF2_HUMAN,,,,,,G,G,xT,L,L,S,V,T,G,E,, +,,sp|P47756|CAPZB_HUMAN,,,,,,,S,xT,L,N,E,I,Y,F,G,, +,,sp|O75937|DNJC8_HUMAN,,,,,,,,xT,F,L,R,P,P,K,,, +,,sp|O15530|PDPK1_HUMAN,,,T,Q,T,E,S,xS,T,P,P,G,I,P,G,, +,,sp|Q99436|PSB7_HUMAN,,,,,T,G,T,xT,I,A,G,V,V,Y,K,, +,,sp|P14625|ENPL_HUMAN,P,E,E,T,A,E,D,xT,T,E,D,T,E,Q,D,, +,,sp|O60508|PRP17_HUMAN,,,,,,S,P,xS,S,K,P,S,L,A,V,, +,,sp|P30086|PEBP1_HUMAN,,N,R,P,T,S,I,xS,W,D,G,L,D,S,G,, +,,sp|O14672|ADA10_HUMAN,,,,,,G,G,xT,F,Y,V,E,P,A,E,, +,,sp|P62701|RS4X_HUMAN; sp|Q8TD47|RS4Y2_HUMAN,,,,,,,L,xT,G,V,F,A,P,R,,, +,,sp|O43491|E41L2_HUMAN,,,,,,S,P,xT,K,A,P,H,L,Q,L,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,I,G,G,I,G,xT,V,P,V,G,R,,,, +,,sp|P78527|PRKDC_HUMAN,,,,,,L,Y,xS,L,A,L,H,P,N,A,, +,,sp|P23246|SFPQ_HUMAN,,,F,A,Q,H,G,xT,F,E,Y,E,Y,S,Q,, +,,sp|P13639|EF2_HUMAN,,,,,,,S,xT,L,T,D,S,L,V,C,, +,,sp|O94826|TOM70_HUMAN,,,,L,R,P,E,xS,A,L,A,Q,A,Q,K,, +,,sp|Q9NUL3|STAU2_HUMAN,,,,V,I,S,G,xT,T,L,G,Y,L,S,P,, +,,sp|P51570|GALK1_HUMAN,E,H,Y,G,G,T,A,xT,F,Y,L,S,Q,A,A,, +,,sp|Q13263|TIF1B_HUMAN,A,A,A,A,S,A,A,xS,G,S,P,G,P,G,E,, +,,sp|Q8ND56|LS14A_HUMAN,,,,,,,,xS,P,V,S,T,R,P,L,, +,,sp|P29401|TKT_HUMAN,,,,,,N,S,xT,F,S,E,I,F,K,K,, +,,sp|Q99832|TCPH_HUMAN,,,,,,,,xT,F,S,Y,A,G,F,E,, +,,sp|Q99873|ANM1_HUMAN,,,,,,,A,xT,L,Y,V,T,A,I,E,, +,,sp|O95433|AHSA1_HUMAN,,,,,,,E,xT,F,L,T,S,P,E,E,, +,,sp|P55265|DSRAD_HUMAN,,,,T,L,P,L,xT,G,S,T,F,H,D,Q,, +,,sp|Q00610|CLH1_HUMAN,,,,,L,A,S,xT,L,V,H,L,G,E,Y,, +,,sp|P53597|SUCA_HUMAN,,,,,G,G,Q,xT,H,L,G,L,P,V,F,, +,,sp|Q00610|CLH1_HUMAN,,,,,,L,A,xS,T,L,V,H,L,G,E,, +,,sp|P49821|NDUV1_HUMAN,,,,,,G,G,xT,W,F,A,G,F,G,R,, +,,sp|P49368|TCPG_HUMAN,,,,,,A,C,xT,I,L,L,R,,,,, +,,sp|P56556|NDUA6_HUMAN,,Q,A,T,S,T,A,xS,T,F,V,K,P,I,F,, +,,sp|Q14C86|GAPD1_HUMAN,T,P,G,L,S,V,V,xS,G,I,S,A,T,S,E,, +,,sp|Q8NF37|PCAT1_HUMAN,,,,,,,I,xT,F,A,D,F,H,R,,, +,,sp|O15530|PDPK1_HUMAN,Q,G,P,A,M,D,G,xT,A,A,E,P,R,,,, +,,sp|C9JLW8|MCRI1_HUMAN,,,,S,P,P,S,xS,S,E,I,F,T,P,A,, +,,sp|Q99829|CPNE1_HUMAN,,,,,,,G,xT,I,T,V,S,A,Q,E,, +,,sp|O15530|PDPK1_HUMAN,,,,,,,,xT,F,F,V,H,T,P,N,, +,,sp|P30041|PRDX6_HUMAN,,,,,,V,A,xT,P,V,D,W,K,,,, +,,sp|P54578|UBP14_HUMAN,,,,,,G,G,xT,L,K,D,D,D,W,G,, +,,sp|Q6UWD8|CP054_HUMAN,,,,Q,R,P,G,xS,P,D,P,E,W,G,L,, +,,sp|P61158|ARP3_HUMAN,I,V,L,S,G,G,S,xT,M,F,R,,,,,, +,,sp|Q13620|CUL4B_HUMAN,,,,,A,F,G,xS,T,I,V,I,N,P,E,, +,,sp|Q00059|TFAM_HUMAN,,,,,,E,L,xT,L,L,G,K,P,K,,, +,,sp|Q16563|SYPL1_HUMAN,,,,T,V,T,A,xT,F,G,Y,P,F,R,,, +,,sp|P08567|PLEK_HUMAN,,,,,,,G,xS,T,L,T,S,P,C,Q,, +,,sp|Q15366|PCBP2_HUMAN,,,,,P,S,S,xS,P,V,I,F,A,G,G,, +,,sp|P25098|ARBK1_HUMAN,,,,,,,,xS,P,V,V,E,L,S,K,, +,,sp|Q86U90|YRDC_HUMAN,,,L,F,R,P,P,xS,P,A,P,A,A,P,G,, +,,sp|P00338|LDHA_HUMAN,,,,,,A,D,xT,L,W,G,I,Q,K,,, +,,sp|P52209|6PGD_HUMAN,,,,,,,,xT,I,F,Q,G,I,A,A,, +,,sp|Q9UQ35|SRRM2_HUMAN,S,E,P,G,T,T,S,xT,Q,R,P,S,S,P,E,, +,,sp|Q6PI48|SYDM_HUMAN,,,,,R,Q,N,xT,F,L,V,L,R,,,, +,,sp|P63010|AP2B1_HUMAN,,,,G,L,E,I,xS,G,T,F,T,H,R,,, +,,sp|P14625|ENPL_HUMAN,A,E,D,T,T,E,D,xT,E,Q,D,E,D,E,E,, +,,sp|Q13283|G3BP1_HUMAN,,,,,Q,Y,Y,xT,L,L,N,Q,A,P,D,, +,,sp|P12956|XRCC6_HUMAN,,,,,,L,G,xS,L,V,D,E,F,K,,, +,,sp|Q9Y617|SERC_HUMAN,,,,,,F,G,xT,I,N,I,V,H,P,K,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,,W,H,H,xT,F,Y,N,E,L,R,,, +,,sp|O94903|PLPHP_HUMAN,,,,,I,G,S,xT,I,F,G,E,R,,,, +,,sp|P32519|ELF1_HUMAN,T,K,P,P,R,P,D,xS,P,A,T,T,P,N,I,, +,,sp|Q13596|SNX1_HUMAN,,,,,A,V,G,xT,Q,T,L,S,G,A,G,, +,,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN,,,,,T,A,G,xT,L,F,G,E,G,F,R,, +,,sp|Q15366|PCBP2_HUMAN,,,,,,P,S,xS,S,P,V,I,F,A,G,, +,,sp|Q6L8Q7|PDE12_HUMAN,,Q,H,E,G,L,A,xT,F,Y,R,,,,,, +,,sp|Q9H0D6|XRN2_HUMAN,,,,,K,Y,P,xS,I,I,V,N,C,V,E,, +,,sp|Q9NZL9|MAT2B_HUMAN,,,,,,,G,xT,F,H,W,S,G,N,E,, +,,sp|Q92841|DDX17_HUMAN,,,,G,T,A,Y,xT,F,F,T,P,G,N,L,, +,,sp|Q2KHR2|RFX7_HUMAN,,,,,S,P,T,xT,V,L,F,T,S,S,P,, +,,sp|P52701|MSH6_HUMAN,,,,,,Q,S,xT,L,Y,S,F,F,P,K,, +,,sp|P26373|RL13_HUMAN,,,,,,V,A,xT,W,F,N,Q,P,A,R,, +,,sp|O75083|WDR1_HUMAN,,,,,,L,Y,xS,I,L,G,T,T,L,K,, +,,sp|P53396|ACLY_HUMAN,,,L,Y,R,P,G,xS,V,A,Y,V,S,R,,, +,,sp|P31146|COR1A_HUMAN,,,,,,K,G,xT,V,V,A,E,K,,,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,S,T,T,xT,G,H,L,I,Y,K,,, +,,sp|Q14181|DPOA2_HUMAN,,,G,Q,V,G,G,xT,F,A,R,,,,,, +,,sp|P13667|PDIA4_HUMAN,,,V,E,G,F,P,xT,I,Y,F,A,P,S,G,, +,,sp|P13861|KAP2_HUMAN,,,,,,A,A,xT,I,V,A,T,S,E,G,, +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN,,,,G,L,A,I,xT,F,V,S,D,E,N,D,, +,,sp|P53396|ACLY_HUMAN,,,,,,G,V,xT,I,I,G,P,A,T,V,, +,,sp|Q71UI9|H2AV_HUMAN; sp|P0C0S5|H2AZ_HUMAN,,,,,,,A,xT,I,A,G,G,G,V,I,, +,,sp|P06733|ENOA_HUMAN,,,,,,,,xT,I,A,P,A,L,V,S,, +,,sp|O60907|TBL1X_HUMAN; sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN,,,,,,,,xT,T,I,I,W,D,A,H,, +,,sp|Q01469|FABP5_HUMAN,,,,,,,,xT,T,Q,F,S,C,T,L,, +,,sp|P05455|LA_HUMAN,,,,,,F,A,xS,D,D,E,H,D,E,H,, +,,sp|P08238|HS90B_HUMAN,,,,,,,,xT,L,T,L,V,D,T,G,, +,,sp|O75534|CSDE1_HUMAN,,,,,G,T,V,xS,F,H,S,H,S,D,H,, +,,sp|P48735|IDHP_HUMAN,,,N,I,L,G,G,xT,V,F,R,,,,,, +,,sp|Q7Z5L9|I2BP2_HUMAN,,R,P,A,S,V,S,xS,S,A,A,V,E,H,E,, +,,sp|O15530|PDPK1_HUMAN,,,,,,A,N,xS,F,V,G,T,A,Q,Y,, +,,sp|Q9HB71|CYBP_HUMAN,,,,,,T,D,xT,V,L,I,L,C,R,,, +,,sp|P14625|ENPL_HUMAN,E,E,T,A,E,D,T,xT,E,D,T,E,Q,D,E,, +,,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN,,,,,I,M,N,xT,F,S,V,V,P,S,P,, +,,sp|P49368|TCPG_HUMAN,,,,,,A,M,xT,G,V,E,Q,W,P,Y,, +,,sp|Q08043|ACTN3_HUMAN; sp|P35609|ACTN2_HUMAN; sp|P12814|ACTN1_HUMAN; sp|O43707|ACTN4_HUMAN,,,,,,,,xT,F,T,A,W,C,N,S,, +,,sp|P00505|AATM_HUMAN,,,,,I,G,A,xS,F,L,Q,R,,,,, +,,sp|Q9NR30|DDX21_HUMAN,,,,,,,,xT,F,H,H,V,Y,S,G,, +,,sp|P09211|GSTP1_HUMAN,,,,,P,P,Y,xT,V,V,Y,F,P,V,R,, +,,sp|P27816|MAP4_HUMAN,,,,,,S,P,xS,T,L,L,P,K,,,, +,,sp|P22626|ROA2_HUMAN,G,F,G,F,V,T,F,xS,S,M,A,E,V,D,A,, +,,sp|Q09472|EP300_HUMAN,,,,,,L,G,xT,F,L,E,N,R,,,, +,,sp|P15880|RS2_HUMAN,,,,,,G,C,xT,A,T,L,G,N,F,A,, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN,,,,,,,,xT,T,P,S,Y,V,A,F,, +,,sp|P12956|XRCC6_HUMAN,,,,,,,R,xT,F,N,T,S,T,G,G,, +,,sp|Q96CW1|AP2M1_HUMAN,,,,,,,,xT,F,I,T,Q,Q,G,I,, +,,sp|Q92769|HDAC2_HUMAN,I,A,C,D,E,E,F,xS,D,S,E,D,E,G,E,, +,,sp|Q9BTE3|MCMBP_HUMAN,,,,,,,N,xS,T,F,T,E,H,L,Y,, +,,sp|Q13126|MTAP_HUMAN,,T,T,M,R,P,Q,xS,F,Y,D,G,S,H,S,, +,,sp|P50452|SPB8_HUMAN; sp|P35237|SPB6_HUMAN,,,,,,T,G,xT,Q,Y,L,L,R,,,, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN,,,S,G,E,V,Y,xT,C,Q,V,E,H,P,S,, +,,sp|P55265|DSRAD_HUMAN,T,L,P,L,T,G,S,xT,F,H,D,Q,I,A,M,, +,,sp|P48444|COPD_HUMAN,,,,,,Q,H,xT,F,V,E,T,E,S,V,, +,,sp|P62191|PRS4_HUMAN,V,A,N,Q,T,S,A,xT,F,L,R,,,,,, +,,sp|Q9NRW3|ABC3C_HUMAN,,,A,M,Y,P,G,xT,F,Y,F,Q,F,K,,, +,,sp|P22681|CBL_HUMAN,,,V,E,R,P,P,xS,P,F,S,M,A,P,Q,, +,,sp|P19338|NUCL_HUMAN,D,D,D,E,E,D,D,xS,E,E,E,A,M,E,T,, +,,sp|Q15084|PDIA6_HUMAN,,,,,,,G,xS,F,S,E,Q,G,I,N,, +,,sp|Q15005|SPCS2_HUMAN,,,,F,F,D,H,xS,G,T,L,V,M,D,A,, +,,sp|Q96JH7|VCIP1_HUMAN,,,,,,,S,xS,T,T,F,F,E,L,Q,, +,,tr|M0R2N4|M0R2N4_HUMAN; sp|Q8WU68|U2AF4_HUMAN; sp|Q01081|U2AF1_HUMAN; sp|P0DN76|U2AF5_HUMAN,,,D,K,V,N,C,xS,F,Y,F,K,,,,, +,,sp|P61158|ARP3_HUMAN,N,I,V,L,S,G,G,xS,T,M,F,R,,,,, +,,sp|Q92608|DOCK2_HUMAN,,,,,,,L,xS,Q,T,F,L,Q,L,S,, +,,sp|P40939|ECHA_HUMAN,,,,,,D,A,xT,L,T,A,L,D,R,,, +,,sp|Q92900|RENT1_HUMAN,T,V,L,Q,R,P,L,xS,L,I,Q,G,P,P,G,, +,,sp|Q02790|FKBP4_HUMAN,,,,,G,E,H,xS,I,V,Y,L,K,P,S,, +,,sp|O14980|XPO1_HUMAN,,,,,,,E,xT,L,V,Y,L,T,H,L,, +,,sp|P18433|PTPRA_HUMAN,,,,,,T,G,xT,F,C,A,L,S,T,V,, +,,sp|P50995|ANX11_HUMAN,,,,,,,G,xT,I,T,D,A,P,G,F,, +,,sp|Q13347|EIF3I_HUMAN,,,,,,D,M,xT,M,F,V,T,A,S,K,, +,,sp|O15511|ARPC5_HUMAN,L,A,A,G,G,V,G,xS,I,V,R,,,,,, +,,sp|P49721|PSB2_HUMAN,,,,Y,Y,T,P,xT,I,S,R,,,,,, +,,sp|Q8ND76|CCNY_HUMAN; sp|Q8N7R7|CCYL1_HUMAN,,,,,,A,S,xT,I,F,L,S,K,,,, +,,sp|P31948|STIP1_HUMAN,,,,,,,,xT,L,L,S,D,P,T,Y,, +,,sp|Q15181|IPYR_HUMAN,G,I,S,C,M,N,T,xT,L,S,E,S,P,F,K,, +,,sp|P50991|TCPD_HUMAN,,,,G,I,H,P,xT,I,I,S,E,S,F,Q,, +,,sp|Q99460|PSMD1_HUMAN,,,S,N,C,K,P,xS,T,F,A,Y,P,A,P,, +,,sp|P62805|H4_HUMAN,,,,,K,T,V,xT,A,M,D,V,V,Y,A,, +,,sp|Q92878|RAD50_HUMAN,,,,,,G,N,xT,F,V,H,D,P,K,,, +,,sp|P13639|EF2_HUMAN,,,,,,,,xT,G,T,I,T,T,F,E,, +,,sp|P14625|ENPL_HUMAN,A,D,D,K,Y,N,D,xT,F,W,K,,,,,, +,,sp|P40926|MDHM_HUMAN,,,,,,A,N,xT,F,V,A,E,L,K,,, +,,sp|P62917|RL8_HUMAN,,A,S,G,N,Y,A,xT,V,I,S,H,N,P,E,, +,,sp|P82650|RT22_HUMAN,,,,,,I,L,xT,P,I,I,F,K,,,, +,,sp|P14866|HNRPL_HUMAN,,,,,T,P,A,xS,P,V,V,H,I,R,,, +,,sp|P29350|PTN6_HUMAN,,,,,,D,G,xT,I,I,H,L,K,,,, +,,sp|P52272|HNRPM_HUMAN,,,G,N,F,G,G,xS,F,A,G,S,F,G,G,, +,,sp|O15530|PDPK1_HUMAN,,T,Q,T,E,S,S,xT,P,P,G,I,P,G,G,, +,,sp|P37268|FDFT_HUMAN,,,,,,Y,Q,xT,V,I,A,D,I,C,R,, +,,sp|Q6UN15|FIP1_HUMAN,,E,R,D,H,S,P,xT,P,S,V,F,N,S,D,, +,,sp|Q9BY44|EIF2A_HUMAN,,,,,,D,G,xT,L,F,A,W,G,N,G,, +,,sp|P06733|ENOA_HUMAN,A,A,V,P,S,G,A,xS,T,G,I,Y,E,A,L,, +,,sp|P07437|TBB5_HUMAN,A,V,T,F,I,G,N,xS,T,A,I,Q,E,L,F,, +,,sp|P06748|NPM_HUMAN,,,,,,L,L,xS,I,S,G,K,,,,, +,,sp|P04406|G3P_HUMAN,,V,P,T,A,N,V,xS,V,V,D,L,T,C,R,, +,,sp|P14314|GLU2B_HUMAN,,,L,G,G,S,P,xT,S,L,G,T,W,G,S,, +,,sp|Q16666|IF16_HUMAN,,,,,,,,xT,T,I,Y,E,I,Q,D,, +,,sp|Q13126|MTAP_HUMAN,,,,,,,G,xT,M,V,T,I,E,G,P,, +,,sp|P07900|HS90A_HUMAN,P,E,I,E,D,V,G,xS,D,E,E,E,E,K,K,, +,,sp|P01911|2B1F_HUMAN; sp|Q30154|DRB5_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,R,, +,,sp|P52272|HNRPM_HUMAN,F,G,G,S,F,A,G,xS,F,G,G,A,G,G,H,, +,,tr|A0A182DWH4|A0A182DWH4_HUMAN,V,E,H,P,S,V,T,xS,P,L,T,V,E,W,S,, +,,sp|O75521|ECI2_HUMAN,A,T,F,H,T,P,F,xS,H,L,G,Q,S,P,E,, +,,sp|Q9BTE3|MCMBP_HUMAN,,,,,,N,S,xT,F,T,E,H,L,Y,R,, +,,sp|P19338|NUCL_HUMAN,A,A,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|P07737|PROF1_HUMAN,,,,,,,,xS,S,F,Y,V,N,G,L,, +,,sp|Q14152|EIF3A_HUMAN,,,,,,L,A,xT,L,L,G,L,Q,A,P,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,A,V,F,P,xS,I,V,G,R,,,,, +,,sp|P00558|PGK1_HUMAN,,,,,G,C,I,xT,I,I,G,G,G,D,T,, +,,sp|Q99832|TCPH_HUMAN,,,,,,,K,xT,F,S,Y,A,G,F,E,, +,,sp|Q86VP6|CAND1_HUMAN,,,,,,L,G,xT,L,S,A,L,D,I,L,, +,,sp|P46940|IQGA1_HUMAN,,,,,,,A,xT,F,Y,G,E,Q,V,D,, +,,sp|Q08211|DHX9_HUMAN,,,,,,G,M,xT,L,V,T,P,L,Q,L,, +,,sp|Q9Y3I0|RTCB_HUMAN,,,,,S,S,M,xT,F,L,T,R,,,,, +,,sp|P04406|G3P_HUMAN,,V,I,I,S,A,P,xS,A,D,A,P,M,F,V,, +,,sp|Q9BRA2|TXD17_HUMAN,,,,,,,,xT,I,F,A,Y,F,T,G,, +,,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN,,,,,,,T,xS,F,F,Q,A,L,G,I,, +,,sp|P49411|EFTU_HUMAN,,,,,,,,xT,T,L,T,A,A,I,T,, +,,sp|O43159|RRP8_HUMAN,,,,Q,R,P,A,xS,L,V,V,A,D,F,G,, +,,sp|P12956|XRCC6_HUMAN,,,,,T,F,N,xT,S,T,G,G,L,L,L,, +,,sp|P43686|PRS6B_HUMAN,,,,,L,I,F,xS,T,I,T,S,K,,,, +,,sp|P54819|KAD2_HUMAN,Q,A,Y,H,T,Q,T,xT,P,L,I,E,Y,Y,R,, +,,sp|P27797|CALR_HUMAN,,,,,,G,Q,xT,L,V,V,Q,F,T,V,, +,,sp|P08559|ODPA_HUMAN,,,,A,H,G,F,xT,F,T,R,,,,,, +,,sp|Q13547|HDAC1_HUMAN,I,A,C,E,E,E,F,xS,D,S,E,E,E,G,E,, +,,sp|Q14697|GANAB_HUMAN,,,,,,,L,xS,F,Q,H,D,P,E,T,, +,,sp|O60508|PRP17_HUMAN,,,,,S,P,S,xS,K,P,S,L,A,V,A,, +,,sp|P07437|TBB5_HUMAN,,,,,M,A,V,xT,F,I,G,N,S,T,A,, +,,sp|Q15084|PDIA6_HUMAN,V,D,A,D,K,H,H,xS,L,G,G,Q,Y,G,V,, +,,sp|O95433|AHSA1_HUMAN,,,,,,,Q,xT,F,G,Y,G,A,R,,, +,,sp|P51991|ROA3_HUMAN,,,,W,G,T,L,xT,D,C,V,V,M,R,D,, +,,sp|Q4KMQ1|TPRN_HUMAN,,,W,Q,R,P,S,xS,P,P,P,F,L,P,A,, +,,sp|P26641|EF1G_HUMAN,,,,,,A,G,xT,L,Y,T,Y,P,E,N,, +,,sp|P09874|PARP1_HUMAN,,,,,,V,G,xT,V,I,G,S,N,K,,, +,,sp|Q9NWH9|SLTM_HUMAN,,,,,,,,xS,P,G,H,M,V,I,L,, +,,sp|P55884|EIF3B_HUMAN,,,,,I,S,V,xS,F,Y,H,V,K,,,, +,,sp|Q99575|POP1_HUMAN,,,,Y,I,T,A,xS,T,F,A,Q,A,R,,, +,,sp|P30086|PEBP1_HUMAN,,,,N,R,P,T,xS,I,S,W,D,G,L,D,, +,,sp|Q15366|PCBP2_HUMAN,P,Y,R,P,K,P,S,xS,S,P,V,I,F,A,G,, +,,sp|O75643|U520_HUMAN,,,,,,S,P,xT,L,Y,G,I,S,H,D,, +,,sp|P15880|RS2_HUMAN,,,,,,,G,xT,G,I,V,S,A,P,V,, +,,sp|P49588|SYAC_HUMAN,,,,,,I,G,xT,I,Y,G,D,L,K,,, +,,sp|Q7Z5L9|I2BP2_HUMAN,R,P,A,S,V,S,S,xS,A,A,V,E,H,E,Q,, +,,sp|P25789|PSA4_HUMAN,,,,,,,,xT,T,I,F,S,P,E,G,, +,,sp|Q9UIA9|XPO7_HUMAN,,,,,,,T,xT,F,Y,T,A,L,G,R,, +,,sp|Q9Y6X4|F169A_HUMAN,,,,,R,P,M,xS,G,E,Y,G,P,A,S,, +,,sp|P22626|ROA2_HUMAN,,,,,,I,D,xT,I,E,I,I,T,D,R,, +,,sp|P07437|TBB5_HUMAN; sp|Q13509|TBB3_HUMAN; tr|A0A0B4J269|A0A0B4J269_HUMAN,G,T,G,S,G,M,G,xT,L,L,I,S,K,,,, +,,sp|O15530|PDPK1_HUMAN,,,I,L,G,E,G,xS,F,S,T,V,V,L,A,, +,,sp|O15042|SR140_HUMAN,,,,,,L,Y,xS,I,L,Q,G,D,S,P,, +,,sp|P62937|PPIA_HUMAN,,,,,V,N,P,xT,V,F,F,D,I,A,V,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,,,,,,xS,P,H,S,P,S,P,I,, +,,sp|P20042|IF2B_HUMAN,,,,,,,,xT,S,F,V,N,F,T,D,, +,,sp|Q9UKM9|RALY_HUMAN,,,,,G,R,L,xS,P,V,P,V,P,R,,, +,,sp|Q2KHR2|RFX7_HUMAN,,,,,,S,P,xT,T,V,L,F,T,S,S,, +,,sp|Q15365|PCBP1_HUMAN,,,,,,A,I,xT,I,A,G,V,P,Q,S,, +,,sp|Q8IYB3|SRRM1_HUMAN,,,,,,,,xS,P,S,P,A,P,P,P,, +,,sp|Q13586|STIM1_HUMAN,,,N,T,L,F,G,xT,F,H,V,A,H,S,S,, +,,sp|Q96JH7|VCIP1_HUMAN,,,,,,,,xS,S,T,T,F,F,E,L,, +,,sp|Q7Z5L9|I2BP2_HUMAN,,,R,P,A,S,V,xS,S,S,A,A,V,E,H,, +,,sp|Q07020|RL18_HUMAN,,T,A,V,V,V,G,xT,I,T,D,D,V,R,,, +,,sp|Q13200|PSMD2_HUMAN,,,,,G,T,L,xT,L,C,P,Y,H,S,D,, +,,sp|Q8WUK0|PTPM1_HUMAN,,,,,,D,G,xT,F,V,I,S,K,,,, +,,sp|Q6NYC8|PPR18_HUMAN,,,,,S,G,H,xT,F,T,V,N,P,R,,, +,,sp|P15498|VAV_HUMAN,,,,,S,D,G,xT,F,L,V,R,,,,, +,,sp|P09651|ROA1_HUMAN; tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN,,,,,,Y,H,xT,V,N,G,H,N,C,E,, +,,sp|Q8IYD1|ERF3B_HUMAN; sp|P15170|ERF3A_HUMAN,,,,,T,A,G,xT,I,C,L,E,T,F,K,, +,,sp|P07737|PROF1_HUMAN,,,,,,,,xT,L,V,L,L,M,G,K,, +,,sp|Q6NYC8|PPR18_HUMAN,,,,,,,,xS,G,H,T,F,T,V,N,, +,,sp|Q8NBQ5|DHB11_HUMAN,,,,,,V,H,xT,F,V,V,D,C,S,N,, +,,sp|Q14C86|GAPD1_HUMAN,L,S,V,V,S,G,I,xS,A,T,S,E,D,I,P,, +,,sp|Q9H7N4|SFR19_HUMAN,,,,Q,R,S,P,xS,P,A,P,A,P,A,P,, +,,sp|P84090|ERH_HUMAN,,,,,,S,H,xT,I,L,L,V,Q,P,T,, +,,sp|P04406|G3P_HUMAN,,,,,V,I,I,xS,A,P,S,A,D,A,P,, +,,sp|Q9Y5K5|UCHL5_HUMAN,,,,,,L,D,xT,I,F,F,A,K,,,, +,,sp|Q68EM7|RHG17_HUMAN,,,,K,R,P,A,xS,M,A,V,M,E,G,D,, +,,sp|Q9HCC0|MCCB_HUMAN,,,,,K,Q,G,xT,I,F,L,A,G,P,P,, +,,sp|Q9UI08|EVL_HUMAN,,,,Y,N,Q,A,xT,P,T,F,H,Q,W,R,, +,,sp|Q13283|G3BP1_HUMAN,,,,,,S,S,xS,P,A,P,A,D,I,A,, +,,sp|Q13177|PAK2_HUMAN,,,,,,,,xS,T,M,V,G,T,P,Y,, +,,sp|P26641|EF1G_HUMAN,,,,,,,,xS,T,F,V,L,D,E,F,, +,,sp|O15530|PDPK1_HUMAN,L,G,E,G,S,F,S,xT,V,V,L,A,R,,,, +,,sp|P20292|AL5AP_HUMAN,,,,,,T,G,xT,L,A,F,E,R,,,, +,,sp|Q99460|PSMD1_HUMAN,,S,N,C,K,P,S,xT,F,A,Y,P,A,P,L,, +,,sp|P20290|BTF3_HUMAN,Q,A,S,L,A,A,N,xT,F,T,I,T,G,H,A,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN; sp|Q9BQE3|TBA1C_HUMAN,G,G,D,D,S,F,N,xT,F,F,S,E,T,G,A,, +,,sp|Q01469|FABP5_HUMAN,,,,,K,T,Q,xT,V,C,N,F,T,D,G,, +,,sp|P47756|CAPZB_HUMAN,,,,,,,,xS,T,L,N,E,I,Y,F,, +,,sp|Q13094|LCP2_HUMAN,,,I,N,Q,D,G,xT,F,L,V,R,,,,, +,,sp|Q9H7N4|SFR19_HUMAN,,,,,,Q,R,xS,P,S,P,A,P,A,P,, +,,sp|P04040|CATA_HUMAN,,,,N,A,I,H,xT,F,V,Q,S,G,S,H,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,I,W,H,H,xT,F,Y,N,E,L,R,,, +,,sp|Q9BWJ5|SF3B5_HUMAN,,,,,,,Y,xT,I,H,S,Q,L,E,H,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,,,,H,xT,F,Y,N,E,L,R,,, +,,sp|P30101|PDIA3_HUMAN,Y,G,V,S,G,Y,P,xT,L,K,,,,,,, +,,sp|Q00839|HNRPU_HUMAN,,,,,,L,N,xT,L,L,Q,R,,,,, +,,sp|Q6ZNL6|FGD5_HUMAN,,,,E,R,P,V,xS,M,S,F,P,L,S,S,, +,,sp|P55265|DSRAD_HUMAN,,T,L,P,L,T,G,xS,T,F,H,D,Q,I,A,, +,,sp|O60573|IF4E2_HUMAN,,,,,Q,I,G,xT,F,A,S,V,E,Q,F,, +,,sp|P52272|HNRPM_HUMAN,,,,,L,G,S,xT,V,F,V,A,N,L,D,, +,,sp|Q9UQ35|SRRM2_HUMAN,F,S,E,P,G,T,T,xS,T,Q,R,P,S,S,P,, +,,sp|Q9BRB3|PIGQ_HUMAN,,,,,,G,G,xT,F,W,S,C,E,A,T,, +,,sp|Q96A35|RM24_HUMAN,,,,,,,G,xT,M,I,P,S,E,A,P,, +,,sp|Q8WV74|NUDT8_HUMAN,,,,A,R,P,A,xS,A,A,V,L,V,P,L,, +,,sp|Q07020|RL18_HUMAN,,,,,T,N,S,xT,F,N,Q,V,V,L,K,, +,,sp|P22626|ROA2_HUMAN,,,G,F,G,F,V,xT,F,D,D,H,D,P,V,, +,,sp|Q15181|IPYR_HUMAN,,,,,,G,I,xS,C,M,N,T,T,L,S,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,,,,A,V,F,P,xS,I,V,G,R,P,R,,, +,,sp|P23246|SFPQ_HUMAN,,,,,,F,A,xT,H,A,A,A,L,S,V,, +,,sp|Q15366|PCBP2_HUMAN,I,P,Y,R,P,K,P,xS,S,S,P,V,I,F,A,, +,,sp|P26641|EF1G_HUMAN,,,,,A,A,G,xT,L,Y,T,Y,P,E,N,, +,,sp|P11142|HSP7C_HUMAN; sp|P0DMV9|HS71B_HUMAN; sp|P0DMV8|HS71A_HUMAN,,,,,T,T,P,xS,Y,V,A,F,T,D,T,, +,,sp|P35269|T2FA_HUMAN,,G,N,S,R,P,G,xT,P,S,A,E,G,G,S,, +,,sp|P49327|FAS_HUMAN,,,,S,F,Y,G,xS,T,L,F,L,C,R,,, +,,sp|Q08945|SSRP1_HUMAN,,,,,,Q,G,xT,Q,Y,T,F,S,S,I,, +,,sp|Q14690|RRP5_HUMAN,,,,,,A,G,xT,Y,F,S,N,Q,A,V,, +,,sp|P07900|HS90A_HUMAN,,,,,,,,xT,L,T,I,V,D,T,G,, +,,sp|O14980|XPO1_HUMAN,,E,T,L,V,Y,L,xT,H,L,D,Y,V,D,T,, +,,sp|P04075|ALDOA_HUMAN,H,E,E,I,A,M,A,xT,V,T,A,L,R,,,, +,,sp|O75521|ECI2_HUMAN,,,,,,,A,xT,F,H,T,P,F,S,H,, +,,sp|P21796|VDAC1_HUMAN,,,,,,,L,xT,F,D,S,S,F,S,P,, +,,sp|Q86VP6|CAND1_HUMAN,,,,,,A,L,xT,L,I,A,G,S,P,L,, +,,sp|P23193|TCEA1_HUMAN,S,A,D,E,P,M,T,xT,F,V,V,C,N,E,C,, +,,sp|P04080|CYTB_HUMAN,,S,Q,V,V,A,G,xT,N,Y,F,I,K,,,, +,,sp|P06748|NPM_HUMAN,D,E,N,E,H,Q,L,xS,L,R,,,,,,, +,,sp|Q96C86|DCPS_HUMAN,,,,,,,,xT,T,V,V,Y,P,A,T,, +,,sp|P61604|CH10_HUMAN,,,,V,L,Q,A,xT,V,V,A,V,G,S,G,, +,,sp|P08865|RSSA_HUMAN,A,S,Y,V,N,L,P,xT,I,A,L,C,N,T,D,, +,,sp|P60709|ACTB_HUMAN; sp|P63261|ACTG_HUMAN,T,V,L,S,G,G,T,xT,M,Y,P,G,I,A,D,, +,,sp|O00461|GOLI4_HUMAN,Y,G,E,N,D,E,N,xT,D,D,K,N,N,D,G,, +,,sp|P19338|NUCL_HUMAN,,,,,,S,I,xS,L,Y,Y,T,G,E,K,, +,,sp|P30086|PEBP1_HUMAN,,,,,,L,Y,xT,L,V,L,T,D,P,D,, +,,sp|O00299|CLIC1_HUMAN,,,,,,G,V,xT,F,N,V,T,T,V,D,, +,,sp|P62807|H2B1C_HUMAN; sp|P57053|H2BFS_HUMAN; sp|O60814|H2B1K_HUMAN; sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|P58876|H2B1D_HUMAN,,,,,E,S,Y,xS,V,Y,V,Y,K,,,, +,,sp|Q15005|SPCS2_HUMAN,,,,,,,L,xT,F,I,S,G,R,,,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/S2.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,524 @@ +Substrates,Species,Reference,X.7,X.6,X.5,X.4,X.3,X.2,X.1,X0,X1,X2,X3,X4,X5,X6,X7,PhosphiteA,B +,,sp|P19338|NUCL_HUMAN,,,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|P13639|EF2_HUMAN,,,,,,T,G,xT,I,T,T,F,E,H,A,, +,,sp|P60709|ACTB_HUMAN,L,Y,A,N,T,V,L,xS,G,G,T,T,M,Y,P,, +,,sp|P11021|BIP_HUMAN,,,,,,,V,xT,H,A,V,V,T,V,P,, +,,sp|P56556|NDUA6_HUMAN,,,,Q,A,T,S,xT,A,S,T,F,V,K,P,, +,,sp|Q9HD20|AT131_HUMAN,,,,,,T,G,xT,L,T,S,D,S,L,V,, +,,sp|Q9UQB8|BAIP2_HUMAN,,,,Q,R,P,Y,xS,V,A,V,P,A,F,S,, +,,sp|Q9UQ35|SRRM2_HUMAN,T,S,T,Q,R,P,S,xS,P,E,T,A,T,K,,, +,,sp|Q06830|PRDX1_HUMAN,,,,,,,,xT,I,A,Q,D,Y,G,V,, +,,sp|P08238|HS90B_HUMAN,,,I,E,D,V,G,xS,D,E,E,D,D,S,G,, +,,sp|Q14974|IMB1_HUMAN,,,,,,,T,xT,L,V,I,M,E,R,,, +,,sp|P29401|TKT_HUMAN,,,,,,N,S,xT,F,S,E,I,F,K,,, +,,sp|Q00839|HNRPU_HUMAN,,,,,,,S,xS,G,P,T,S,L,F,A,, +,,sp|Q16531|DDB1_HUMAN,,,,,,,Q,xS,T,I,V,C,H,N,R,, +,,sp|O15530|PDPK1_HUMAN,,,,,,,,xT,Y,Y,L,M,D,P,S,, +,,sp|Q14258|TRI25_HUMAN,,,,,,F,D,xT,I,Y,Q,I,L,L,K,, +,,sp|P52566|GDIR2_HUMAN,,,,,,,A,xT,F,M,V,G,S,Y,G,, +,,sp|Q9Y5S9|RBM8A_HUMAN,,,,,,G,Y,xT,L,V,E,Y,E,T,Y,, +,,sp|P30086|PEBP1_HUMAN,,,G,N,D,I,S,xS,G,T,V,L,S,D,Y,, +,,sp|P19338|NUCL_HUMAN,,A,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|Q32P44|EMAL3_HUMAN,,,,G,R,P,I,xT,M,Y,I,P,S,G,I,, +,,sp|P29401|TKT_HUMAN,,,,,,,,xS,T,F,A,A,F,F,T,, +,,sp|P41252|SYIC_HUMAN,,,,,,T,G,xT,I,V,V,E,G,H,E,, +,,sp|P28070|PSB4_HUMAN,N,S,T,M,L,G,A,xS,G,D,Y,A,D,F,Q,, +,,sp|P09211|GSTP1_HUMAN,,,,,,,,xT,V,V,Y,F,P,V,R,, +,,sp|P09429|HMGB1_HUMAN; sp|P26583|HMGB2_HUMAN,,,,,R,P,P,xS,A,F,F,L,F,,,, +,,sp|P04083|ANXA1_HUMAN,S,A,V,S,P,Y,P,xT,F,N,P,S,S,D,V,, +,,sp|P07900|HS90A_HUMAN; sp|P08238|HS90B_HUMAN,,,,,,S,L,xT,N,D,W,E,D,H,L,, +,,sp|P49321|NASP_HUMAN,G,S,G,D,A,V,P,xS,G,N,E,V,S,E,N,, +,,sp|P07437|TBB5_HUMAN,V,T,F,I,G,N,S,xT,A,I,Q,E,L,F,K,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN,D,V,N,A,A,I,A,xT,I,K,,,,,,, +,,sp|P14625|ENPL_HUMAN,P,E,E,E,P,E,E,xT,A,E,D,T,T,E,D,, +,,sp|P10075|GLI4_HUMAN,,,,,,,,xS,P,G,S,Q,A,P,D,, +,,sp|Q14554|PDIA5_HUMAN,,,,,G,Y,P,xT,F,H,Y,Y,H,Y,G,, +,,sp|Q9Y266|NUDC_HUMAN,,L,I,T,Q,T,F,xS,H,H,N,Q,L,A,Q,, +,,sp|P06748|NPM_HUMAN,,,,,,T,V,xS,L,G,A,G,A,K,,, +,,sp|O75534|CSDE1_HUMAN,,,,,,L,L,xT,S,Y,G,F,I,Q,C,, +,,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN,,,,,,,,xT,S,F,F,Q,A,L,G,, +,,sp|P07814|SYEP_HUMAN,,A,I,Q,G,G,T,xS,H,H,L,G,Q,N,F,, +,,sp|Q00613|HSF1_HUMAN,D,T,E,G,R,P,P,xS,P,P,P,T,S,T,P,, +,,sp|P47712|PA24A_HUMAN,,,,,,Y,G,xT,F,M,A,P,D,L,F,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN,T,I,G,G,G,D,D,xS,F,N,T,F,F,S,E,, +,,sp|P53597|SUCA_HUMAN,,,,,,Q,G,xT,F,H,S,Q,Q,A,L,, +,,sp|P07237|PDIA1_HUMAN,,,,,,V,H,xS,F,P,T,L,K,,,, +,,sp|Q96A26|F162A_HUMAN,,,,,,H,E,xT,L,T,S,L,N,L,E,, +,,sp|P51570|GALK1_HUMAN,I,Q,E,H,Y,G,G,xT,A,T,F,Y,L,S,Q,, +,,sp|P30101|PDIA3_HUMAN,,,,,G,F,P,xT,I,Y,F,S,P,A,N,, +,,sp|P23193|TCEA1_HUMAN; sp|Q15560|TCEA2_HUMAN,,,,,T,G,G,xT,Q,T,D,L,F,T,C,, +,,sp|Q16851|UGPA_HUMAN,,,,,,I,Y,xT,F,N,Q,S,R,,,, +,,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN,,,,,,A,G,xT,L,F,G,E,G,F,R,, +,,sp|Q4KMQ1|TPRN_HUMAN,,,,W,Q,R,P,xS,S,P,P,P,F,L,P,, +,,sp|Q13200|PSMD2_HUMAN,,,,,,,G,xT,L,T,L,C,P,Y,H,, +,,sp|Q9UQ35|SRRM2_HUMAN,,,,,,,,xS,P,V,P,S,A,F,S,, +,,sp|O43776|SYNC_HUMAN,,,,K,E,D,G,xT,F,Y,E,F,G,E,D,, +,,sp|Q9HCC0|MCCB_HUMAN,,,,,,Q,G,xT,I,F,L,A,G,P,P,, +,,sp|P42166|LAP2A_HUMAN,,,,,,G,G,xT,L,F,G,G,E,V,C,, +,,sp|O43760|SNG2_HUMAN,,,,,A,G,G,xS,F,D,L,R,,,,, +,,sp|P30086|PEBP1_HUMAN,G,N,D,I,S,S,G,xT,V,L,S,D,Y,V,G,, +,,sp|P19338|NUCL_HUMAN,,,,V,A,V,A,xT,P,A,K,K,,,,, +,,sp|Q8TD47|RS4Y2_HUMAN; sp|P62701|RS4X_HUMAN,,,,,,,L,xT,I,A,E,E,R,,,, +,,sp|P07900|HS90A_HUMAN,,,,D,K,E,V,xS,D,D,E,A,E,E,K,, +,,sp|Q6UN15|FIP1_HUMAN,,,,E,R,D,H,xS,P,T,P,S,V,F,N,, +,,sp|P40926|MDHM_HUMAN,,A,G,A,G,S,A,xT,L,S,M,A,Y,A,G,, +,,sp|P00387|NB5R3_HUMAN,N,L,V,V,R,P,Y,xT,P,I,S,S,D,D,D,, +,,sp|P07737|PROF1_HUMAN,,,,,,,S,xS,F,Y,V,N,G,L,T,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,,,S,P,H,xS,P,S,P,I,A,T,P,, +,,sp|P49189|AL9A1_HUMAN,,,,,V,I,A,xT,F,T,C,S,G,E,K,, +,,sp|P42166|LAP2A_HUMAN,,,,,,S,S,xT,P,L,P,T,I,S,S,, +,,sp|P62942|FKB1A_HUMAN,,,,,R,G,Q,xT,C,V,V,H,Y,T,G,, +,,sp|P11021|BIP_HUMAN,,,,,,,I,xT,P,S,Y,V,A,F,T,, +,,sp|O60934|NBN_HUMAN,,,,,,Y,G,xT,F,V,N,E,E,K,,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,,,Q,xT,V,A,V,G,V,I,K,, +,,sp|P63244|RACK1_HUMAN,,,,,,D,K,xT,I,I,M,W,K,,,, +,,sp|Q92900|RENT1_HUMAN,,,,,T,V,T,xS,A,T,I,V,Y,H,L,, +,,sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN; sp|O60907|TBL1X_HUMAN,,,,,,,T,xT,I,I,W,D,A,H,T,, +,,sp|P37198|NUP62_HUMAN,,,,E,Q,S,G,xT,I,Y,L,Q,H,A,D,, +,,sp|Q6ZT62|BGIN_HUMAN; sp|Q9Y3L3|3BP1_HUMAN,,,,,,,,xS,P,P,E,T,A,A,P,, +,,sp|P60709|ACTB_HUMAN,,,D,L,Y,A,N,xT,V,L,S,G,G,T,T,, +,,sp|P60709|ACTB_HUMAN,,,,,,E,I,xT,A,L,A,P,S,T,M,, +,,sp|P26641|EF1G_HUMAN,,,,,,,S,xT,F,V,L,D,E,F,K,, +,,sp|Q92974|ARHG2_HUMAN,,,,E,R,P,S,xS,A,I,Y,P,S,D,S,, +,,sp|P49189|AL9A1_HUMAN,,,,,S,T,G,xT,F,V,V,S,Q,P,L,, +,,sp|P33241|LSP1_HUMAN,,,,,,,,xS,P,E,G,E,Q,E,D,, +,,sp|Q9BVA1|TBB2B_HUMAN; sp|Q13885|TBB2A_HUMAN; sp|P68371|TBB4B_HUMAN,,,,,M,S,A,xT,F,I,G,N,S,T,A,, +,,sp|P07900|HS90A_HUMAN,,,,,,T,L,xT,I,V,D,T,G,I,G,, +,,sp|Q9NP66|HM20A_HUMAN,,,,,,,,xS,P,L,T,G,Y,V,R,, +,,sp|Q96I25|SPF45_HUMAN,S,P,T,G,P,S,N,xS,F,L,A,N,M,G,G,, +,,sp|Q92841|DDX17_HUMAN,,,,,,,G,xT,A,Y,T,F,F,T,P,, +,,sp|Q7KZF4|SND1_HUMAN,,,,,,L,G,xT,L,S,P,A,F,S,T,, +,,sp|P11142|HSP7C_HUMAN,,,,,,,G,xT,L,D,P,V,E,K,,, +,,sp|P51991|ROA3_HUMAN; sp|P09651|ROA1_HUMAN,,,,,,W,G,xT,L,T,D,C,V,V,M,, +,,sp|P55263|ADK_HUMAN,,,,,,A,A,xT,F,F,G,C,I,G,I,, +,,sp|Q96FV9|THOC1_HUMAN,,,,,,S,N,xT,F,Y,S,A,G,K,,, +,,sp|Q92499|DDX1_HUMAN,N,T,R,P,G,A,N,xS,P,E,M,W,S,E,A,, +,,sp|Q01082|SPTB2_HUMAN,,,,,R,P,P,xS,P,E,P,S,T,K,,, +,,sp|P49327|FAS_HUMAN,,,,,V,Y,A,xT,I,L,N,A,G,T,N,, +,,sp|Q9UQ35|SRRM2_HUMAN,A,P,F,S,E,P,G,xT,T,S,T,Q,R,P,S,, +,,sp|C9JLW8|MCRI1_HUMAN,,,S,P,P,S,S,xS,E,I,F,T,P,A,H,, +,,sp|P63167|DYL1_HUMAN; sp|Q96FJ2|DYL2_HUMAN,,,,,Y,N,P,xT,W,H,C,I,V,G,R,, +,,sp|Q969T9|WBP2_HUMAN,,,,,,K,G,xT,V,Y,L,T,P,Y,R,, +,,sp|P07195|LDHB_HUMAN,,,,,S,A,D,xT,L,W,D,I,Q,K,,, +,,sp|Q9Y678|COPG1_HUMAN,,,,,,,A,xT,F,Y,L,N,V,L,E,, +,,sp|P07437|TBB5_HUMAN,,,,,,,I,xS,V,Y,Y,N,E,A,T,, +,,sp|P62888|RL30_HUMAN,,,,,,V,C,xT,L,A,I,I,D,P,G,, +,,sp|P60709|ACTB_HUMAN,E,I,T,A,L,A,P,xS,T,M,K,,,,,, +,,sp|P06748|NPM_HUMAN,A,V,E,E,D,A,E,xS,E,D,E,E,E,E,D,, +,,sp|Q14161|GIT2_HUMAN,,,,,,,G,xT,F,L,C,D,E,C,C,, +,,sp|Q15084|PDIA6_HUMAN,V,G,G,G,A,F,P,xT,I,V,E,R,,,,, +,,sp|P30086|PEBP1_HUMAN,,,,G,N,D,I,xS,S,G,T,V,L,S,D,, +,,sp|Q9UQ35|SRRM2_HUMAN,P,F,S,E,P,G,T,xT,S,T,Q,R,P,S,S,, +,,sp|Q92608|DOCK2_HUMAN,,,,,L,S,Q,xT,F,L,Q,L,S,D,G,, +,,sp|Q15019|SEPT2_HUMAN,Y,H,L,P,D,A,E,xS,D,E,D,E,D,F,K,, +,,sp|Q15185|TEBP_HUMAN,,,,,,,L,xT,F,S,C,L,G,G,S,, +,,sp|O75964|ATP5L_HUMAN,,,,,,L,A,xT,F,W,Y,Y,A,K,,, +,,sp|Q15370|ELOB_HUMAN,,,,,,,T,xT,I,F,T,D,A,K,,, +,,sp|O95218|ZRAB2_HUMAN,,E,V,E,D,K,E,xS,E,G,E,E,E,D,E,, +,,sp|P15531|NDKA_HUMAN; sp|P22392|NDKB_HUMAN,,,,,,,,xT,F,I,A,I,K,P,D,, +,,sp|O00461|GOLI4_HUMAN,L,E,H,N,A,E,E,xT,Y,G,E,N,D,E,N,, +,,sp|P10809|CH60_HUMAN,,,,,,,,xT,V,I,I,E,Q,S,W,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,,Y,V,xT,I,I,D,A,P,G,H,, +,,sp|P25705|ATPA_HUMAN,,,,,,T,G,xT,A,E,M,S,S,I,L,, +,,sp|P04083|ANXA1_HUMAN,G,G,P,G,S,A,V,xS,P,Y,P,T,F,N,P,, +,,sp|P00558|PGK1_HUMAN,Y,V,N,D,A,F,G,xT,A,H,R,,,,,, +,,sp|P60709|ACTB_HUMAN,N,T,V,L,S,G,G,xT,T,M,Y,P,G,I,A,, +,,sp|Q02878|RL6_HUMAN,,A,S,I,T,P,G,xT,I,L,I,I,L,T,G,, +,,sp|P46776|RL27A_HUMAN,,,,,,L,W,xT,L,V,S,E,Q,T,R,, +,,sp|P54105|ICLN_HUMAN,,,G,L,G,T,G,xT,L,Y,I,A,E,S,R,, +,,sp|Q06830|PRDX1_HUMAN,,,,,,,A,xT,A,V,M,P,D,G,Q,, +,,sp|P12236|ADT3_HUMAN; sp|Q9H0C2|ADT4_HUMAN; sp|P12235|ADT1_HUMAN; sp|P05141|ADT2_HUMAN,,,,,Y,F,P,xT,Q,A,L,N,F,A,F,, +,,sp|Q9UJ68|MSRA_HUMAN,,,,,E,G,Q,xT,F,Y,Y,A,E,D,Y,, +,,sp|P25705|ATPA_HUMAN,,,,,,,,xT,G,T,A,E,M,S,S,, +,,sp|Q16629|SRSF7_HUMAN,,,,,,A,F,xS,Y,Y,G,P,L,R,,, +,,sp|P17480|UBF1_HUMAN,,,,,R,P,V,xS,A,M,F,I,F,S,E,, +,,sp|P62906|RL10A_HUMAN,,,,,,,D,xT,L,Y,E,A,V,R,,, +,,sp|Q00610|CLH1_HUMAN,,,,,,A,H,xT,M,T,D,D,V,T,F,, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN,,,,,,R,V,xT,I,M,P,K,,,,, +,,sp|P49411|EFTU_HUMAN,,G,T,V,V,T,G,xT,L,E,R,,,,,, +,,sp|Q10567|AP1B1_HUMAN,,,,G,L,E,I,xS,G,T,F,T,R,,,, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN,,,,,,,Q,xT,L,M,W,S,A,T,W,, +,,sp|P17844|DDX5_HUMAN,,,T,G,T,A,Y,xT,F,F,T,P,N,N,I,, +,,sp|Q7L014|DDX46_HUMAN,,,,,,G,G,xT,I,L,A,P,T,V,S,, +,,sp|P37802|TAGL2_HUMAN,,,,,I,Q,A,xS,T,M,A,F,K,,,, +,,sp|P11940|PABP1_HUMAN,,E,F,S,P,F,G,xT,I,T,S,A,K,,,, +,,sp|Q9H1E3|NUCKS_HUMAN,,,A,T,V,T,P,xS,P,V,K,,,,,, +,,sp|Q9BVA1|TBB2B_HUMAN; sp|Q13885|TBB2A_HUMAN; sp|P68371|TBB4B_HUMAN,S,A,T,F,I,G,N,xS,T,A,I,Q,E,L,F,, +,,sp|Q8TBC3|SHKB1_HUMAN,,,,,R,P,P,xT,P,A,P,W,P,S,S,, +,,sp|Q53H96|P5CR3_HUMAN,D,V,C,T,P,G,G,xT,T,I,Y,G,L,H,A,, +,,sp|C9JLW8|MCRI1_HUMAN,,,,,S,P,P,xS,S,S,E,I,F,T,P,, +,,sp|Q6PJG2|EMSA1_HUMAN,,,,,,A,G,xT,F,I,A,P,P,V,Y,, +,,sp|Q9BWW4|SSBP3_HUMAN; sp|Q9BWG4|SSBP4_HUMAN; sp|P81877|SSBP2_HUMAN,,,,,S,A,Q,xT,F,L,S,E,I,R,,, +,,sp|Q8N8J7|F241A_HUMAN,,,,,,M,G,xT,L,F,G,E,L,N,K,, +,,sp|Q92974|ARHG2_HUMAN,,,,,E,R,P,xS,S,A,I,Y,P,S,D,, +,,sp|P14625|ENPL_HUMAN,A,K,E,E,K,E,E,xS,D,D,E,A,A,V,E,, +,,sp|P15880|RS2_HUMAN,,,,G,C,T,A,xT,L,G,N,F,A,K,,, +,,sp|P00338|LDHA_HUMAN,,,,,,,V,xT,L,T,S,E,E,E,A,, +,,sp|P31943|HNRH1_HUMAN,,,Y,G,D,G,G,xS,T,F,Q,S,T,T,G,, +,,sp|Q8NC51|PAIRB_HUMAN,,,,,,,S,xS,F,S,H,Y,S,G,L,, +,,sp|O15530|PDPK1_HUMAN,,,,T,Q,T,E,xS,S,T,P,P,G,I,P,, +,,sp|P28070|PSB4_HUMAN,,,,,V,N,N,xS,T,M,L,G,A,S,G,, +,,sp|P56556|NDUA6_HUMAN,Q,A,T,S,T,A,S,xT,F,V,K,P,I,F,S,, +,,sp|P00558|PGK1_HUMAN,C,A,N,P,A,A,G,xS,V,I,L,L,E,N,L,, +,,sp|P07900|HS90A_HUMAN; sp|P08238|HS90B_HUMAN,,,,,,Y,E,xS,L,T,D,P,S,K,,, +,,sp|P06733|ENOA_HUMAN,A,V,P,S,G,A,S,xT,G,I,Y,E,A,L,E,, +,,sp|P20042|IF2B_HUMAN,,,,,,,T,xS,F,V,N,F,T,D,I,, +,,sp|P54886|P5CS_HUMAN,,,,,,V,G,xT,F,F,S,E,V,K,P,, +,,sp|P00558|PGK1_HUMAN,,,,T,G,Q,A,xT,V,A,S,G,I,P,A,, +,,sp|Q92541|RTF1_HUMAN,,,T,S,E,V,Y,xS,D,D,E,E,E,E,E,, +,,sp|O15120|PLCB_HUMAN,,,,,,,T,xT,F,L,H,I,S,K,,, +,,sp|Q9NSD9|SYFB_HUMAN,,,,,,T,Y,xT,I,A,N,Q,F,P,L,, +,,sp|Q16666|IF16_HUMAN,,,,,,,T,xT,I,Y,E,I,Q,D,D,, +,,sp|Q13423|NNTM_HUMAN,,,,,,G,I,xT,H,I,G,Y,T,D,L,, +,,sp|P13639|EF2_HUMAN,,,,,,,,xS,T,L,T,D,S,L,V,, +,,sp|O15530|PDPK1_HUMAN,,,,P,G,A,G,xS,L,Q,H,A,Q,P,P,, +,,sp|P11940|PABP1_HUMAN,K,E,F,S,P,F,G,xT,I,T,S,A,K,,,, +,,sp|Q9BT22|ALG1_HUMAN; sp|C9J202|AG1L2_HUMAN,,,,,,A,V,xT,V,Y,D,K,P,A,S,, +,,sp|O75746|CMC1_HUMAN,,,,L,A,T,A,xT,F,A,G,I,E,N,K,, +,,sp|P30086|PEBP1_HUMAN,,,,,N,R,P,xT,S,I,S,W,D,G,L,, +,,sp|P37198|NUP62_HUMAN,,,,,,E,Q,xS,G,T,I,Y,L,Q,H,, +,,sp|P51991|ROA3_HUMAN,,,,,,Y,H,xT,I,N,G,H,N,C,E,, +,,sp|P47897|SYQ_HUMAN,,G,H,N,T,L,P,xS,P,W,R,,,,,, +,,sp|Q15366|PCBP2_HUMAN,Y,R,P,K,P,S,S,xS,P,V,I,F,A,G,G,, +,,sp|O15530|PDPK1_HUMAN,,,,,N,F,K,xT,F,F,V,H,T,P,N,, +,,sp|P50748|KNTC1_HUMAN,,,,,,L,T,xT,F,Y,G,A,F,G,P,, +,,sp|Q9UQ35|SRRM2_HUMAN,T,T,S,T,Q,R,P,xS,S,P,E,T,A,T,K,, +,,sp|Q8N6L1|KTAP2_HUMAN,,,,,I,S,S,xT,L,Y,Q,A,A,A,P,, +,,sp|P00558|PGK1_HUMAN,,,,,A,H,S,xS,M,V,G,V,N,L,P,, +,,sp|Q7Z5L9|I2BP2_HUMAN,,,,,R,K,P,xS,P,E,P,E,G,E,V,, +,,sp|P09429|HMGB1_HUMAN,,,,,R,P,P,xS,A,F,F,L,F,C,S,, +,,sp|P49321|NASP_HUMAN,V,P,S,G,N,E,V,xS,E,N,M,E,E,E,A,, +,,sp|Q13523|PRP4B_HUMAN,,,,,,,,xS,P,I,I,N,E,S,R,, +,,sp|P22681|CBL_HUMAN,E,R,P,P,S,P,F,xS,M,A,P,Q,A,S,L,, +,,sp|P28066|PSA5_HUMAN,F,H,M,D,P,S,G,xT,F,V,Q,C,D,A,R,, +,,sp|P06748|NPM_HUMAN,E,A,M,N,Y,E,G,xS,P,I,K,,,,,, +,,sp|P22626|ROA2_HUMAN,,,,,,Y,H,xT,I,N,G,H,N,A,E,, +,,sp|Q16851|UGPA_HUMAN,,,,,,,G,xT,V,I,I,I,A,N,H,, +,,sp|Q5H9R7|PP6R3_HUMAN,,,,,,W,E,xT,F,C,T,S,S,L,G,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,Y,Y,V,xT,I,I,D,A,P,G,H,, +,,sp|P18031|PTN1_HUMAN,,,,Y,R,D,V,xS,P,F,D,H,S,R,,, +,,sp|P47756|CAPZB_HUMAN,,,,,,S,G,xS,G,T,M,N,L,G,G,, +,,sp|O15530|PDPK1_HUMAN,E,P,R,P,G,A,G,xS,L,Q,H,A,Q,P,P,, +,,sp|P49411|EFTU_HUMAN,,,,,,,T,xT,L,T,A,A,I,T,K,, +,,sp|P11021|BIP_HUMAN,,,,,I,T,P,xS,Y,V,A,F,T,P,E,, +,,sp|P08236|BGLR_HUMAN,,,,S,L,D,P,xS,R,P,V,T,F,V,S,, +,,sp|P06744|G6PI_HUMAN,,,,,T,F,T,xT,Q,E,T,I,T,N,A,, +,,sp|P27824|CALX_HUMAN,,,,,,,G,xT,L,S,G,W,I,L,S,, +,,sp|Q86YP4|P66A_HUMAN,,,,,R,P,P,xS,P,D,V,I,V,L,S,, +,,sp|O15530|PDPK1_HUMAN,,,,,,T,Q,xT,E,S,S,T,P,P,G,, +,,sp|E9PAV3|NACAM_HUMAN,,,S,P,A,S,D,xT,Y,I,V,F,G,E,A,, +,,sp|P51858|HDGF_HUMAN,A,G,D,L,L,E,D,xS,P,K,,,,,,, +,,sp|O95340|PAPS2_HUMAN; sp|O43252|PAPS1_HUMAN,,,,,,G,C,xT,V,W,L,T,G,L,S,, +,,sp|Q14978|NOLC1_HUMAN,,,,,,,,xS,P,A,V,K,P,A,A,, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN,,,,,,,S,xT,C,I,Y,G,G,A,P,, +,,sp|Q2KHR2|RFX7_HUMAN,,,,,,,,xS,P,T,T,V,L,F,T,, +,,sp|P49189|AL9A1_HUMAN,,,,,,M,S,xT,G,T,F,V,V,S,Q,, +,,sp|B0I1T2|MYO1G_HUMAN,,,,,,,G,xS,F,T,L,L,W,P,S,, +,,sp|P25787|PSA2_HUMAN,,,,,,G,Y,xS,F,S,L,T,T,F,S,, +,,sp|O00154|BACH_HUMAN,A,G,N,V,H,G,G,xT,I,L,K,,,,,, +,,sp|P17844|DDX5_HUMAN; sp|Q92841|DDX17_HUMAN,,,,,,,,xS,T,C,I,Y,G,G,A,, +,,sp|Q8IY67|RAVR1_HUMAN,L,S,A,V,H,S,P,xT,F,C,Q,L,A,C,G,, +,,sp|Q68EM7|RHG17_HUMAN,,,,,R,P,A,xS,M,A,V,M,E,G,D,, +,,sp|Q9Y266|NUDC_HUMAN,,,,L,I,T,Q,xT,F,S,H,H,N,Q,L,, +,,sp|Q9NVV0|TM38B_HUMAN,,,,G,A,G,G,xT,I,I,T,N,F,E,R,, +,,sp|P08567|PLEK_HUMAN,,,,,,G,S,xT,L,T,S,P,C,Q,D,, +,,sp|Q9UKW4|VAV3_HUMAN,,,,,,,G,xT,F,Y,Q,G,Y,L,C,, +,,tr|K7EKS7|K7EKS7_HUMAN; sp|P35268|RL22_HUMAN,,,,,,,I,xT,V,T,S,E,V,P,F,, +,,sp|P21439|MDR3_HUMAN; sp|P08183|MDR1_HUMAN,,,,,,,T,xT,I,V,I,A,H,R,,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,S,P,H,S,P,xS,P,I,A,T,P,P,S,, +,,sp|P00352|AL1A1_HUMAN,,,,,A,N,N,xT,F,Y,G,L,S,A,G,, +,,sp|Q9Y266|NUDC_HUMAN,,,,,,L,I,xT,Q,T,F,S,H,H,N,, +,,sp|P19338|NUCL_HUMAN,,,,,,,V,xT,L,D,W,A,K,P,K,, +,,sp|Q53H96|P5CR3_HUMAN,V,C,T,P,G,G,T,xT,I,Y,G,L,H,A,L,, +,,sp|P52701|MSH6_HUMAN,,,,,,,Q,xS,T,L,Y,S,F,F,P,, +,,sp|Q01130|SRSF2_HUMAN,,,,,,S,R,xS,P,P,P,V,S,K,,, +,,sp|Q7KZF4|SND1_HUMAN,V,D,Y,I,R,P,A,xS,P,A,T,E,T,V,P,, +,,sp|Q5TC12|ATPF1_HUMAN,,,A,Q,S,C,P,xT,F,L,C,A,L,P,R,, +,,sp|P35244|RFA3_HUMAN,,,,,,,A,xT,I,L,C,T,S,Y,V,, +,,sp|Q96C86|DCPS_HUMAN,,,,,,,T,xT,V,V,Y,P,A,T,E,, +,,tr|A0A096LPI6|A0A096LPI6_HUMAN; sp|P0DPI2|GAL3A_HUMAN; sp|A0A0B4J2D5|GAL3B_HUMAN,,,,,,N,L,xS,T,F,A,V,D,G,K,, +,,sp|Q00839|HNRPU_HUMAN,,,,S,S,G,P,xT,S,L,F,A,V,T,V,, +,,sp|Q16563|SYPL1_HUMAN,,,,,,T,V,xT,A,T,F,G,Y,P,F,, +,,sp|E9PAV3|NACAM_HUMAN,,,,,S,P,A,xS,D,T,Y,I,V,F,G,, +,,sp|Q16851|UGPA_HUMAN,,,,,,G,G,xT,L,T,Q,Y,E,G,K,, +,,sp|P78371|TCPB_HUMAN,,,,,,L,T,xS,F,I,G,A,I,A,I,, +,,sp|P16150|LEUK_HUMAN,,,R,P,T,L,T,xT,F,F,G,R,,,,, +,,sp|P62263|RS14_HUMAN,,,A,S,F,N,D,xT,F,V,H,V,T,D,L,, +,,sp|P49406|RM19_HUMAN,,,,G,L,G,A,xT,F,I,L,R,,,,, +,,sp|P45880|VDAC2_HUMAN,,,,,,,L,xT,F,D,T,T,F,S,P,, +,,sp|P60174|TPIS_HUMAN,,,,D,C,G,A,xT,W,V,V,L,G,H,S,, +,,sp|P08236|BGLR_HUMAN,L,D,P,S,R,P,V,xT,F,V,S,N,S,N,Y,, +,,sp|P51692|STA5B_HUMAN; sp|P42229|STA5A_HUMAN,,,,,,,A,xT,I,I,S,E,Q,Q,A,, +,,sp|P06733|ENOA_HUMAN,,,,A,A,V,P,xS,G,A,S,T,G,I,Y,, +,,sp|P48735|IDHP_HUMAN,E,A,E,A,A,H,G,xT,V,T,R,,,,,, +,,sp|P29401|TKT_HUMAN,,,,,,,S,xT,F,A,A,F,F,T,R,, +,,sp|P47756|CAPZB_HUMAN,,,,S,G,S,G,xT,M,N,L,G,G,S,L,, +,,sp|P49189|AL9A1_HUMAN,,,,M,S,T,G,xT,F,V,V,S,Q,P,L,, +,,sp|O00567|NOP56_HUMAN,,L,I,A,H,A,G,xS,L,T,N,L,A,K,,, +,,sp|Q9UQ35|SRRM2_HUMAN,Q,S,H,S,G,S,I,xS,P,Y,P,K,,,,, +,,sp|P11142|HSP7C_HUMAN,,,,,D,A,G,xT,I,A,G,L,N,V,L,, +,,sp|P11021|BIP_HUMAN,,,,,D,A,G,xT,I,A,G,L,N,V,M,, +,,sp|O00541|PESC_HUMAN,,,,E,R,Y,P,xT,F,I,D,A,L,R,,, +,,sp|P08238|HS90B_HUMAN,,,,,,T,L,xT,L,V,D,T,G,I,G,, +,,sp|P35249|RFC4_HUMAN,,,,,,A,I,xT,F,L,Q,S,A,T,R,, +,,sp|P19338|NUCL_HUMAN,,,,K,V,V,V,xS,P,T,K,K,,,,, +,,sp|Q53H96|P5CR3_HUMAN,,,,S,D,V,C,xT,P,G,G,T,T,I,Y,, +,,sp|P62081|RS7_HUMAN,,,,,,V,E,xT,F,S,G,V,Y,K,,, +,,sp|Q9Y490|TLN1_HUMAN,,,,E,G,T,E,xT,F,A,D,H,R,,,, +,,sp|Q92900|RENT1_HUMAN,,,T,V,T,S,A,xT,I,V,Y,H,L,A,R,, +,,sp|P05455|LA_HUMAN,,,,,,,,xS,P,S,K,P,L,P,E,, +,,sp|Q92900|RENT1_HUMAN,,,,,,T,V,xT,S,A,T,I,V,Y,H,, +,,tr|H7C0C1|H7C0C1_HUMAN; sp|P48047|ATPO_HUMAN,,,,,,Y,A,xT,A,L,Y,S,A,A,S,, +,,sp|P26373|RL13_HUMAN,,,,,,L,A,xT,Q,L,T,G,P,V,M,, +,,sp|Q9Y3D7|TIM16_HUMAN,,,,S,V,G,G,xS,F,Y,L,Q,S,K,,, +,,sp|P00338|LDHA_HUMAN,,,,,S,A,D,xT,L,W,G,I,Q,K,,, +,,sp|P55884|EIF3B_HUMAN,,,,,,,V,xT,L,M,Q,L,P,T,R,, +,,sp|Q13564|ULA1_HUMAN,,,,,,,Q,xT,P,S,F,W,I,L,A,, +,,sp|Q16658|FSCN1_HUMAN,Y,L,A,P,S,G,P,xS,G,T,L,K,,,,, +,,sp|Q9HC35|EMAL4_HUMAN,,,,G,R,P,I,xT,M,F,I,P,S,D,V,, +,,sp|P29590|PML_HUMAN,,,,,,T,P,xT,L,T,S,I,Y,C,R,, +,,sp|P00505|AATM_HUMAN,,,,V,G,A,F,xT,M,V,C,K,,,,, +,,sp|P31943|HNRH1_HUMAN,,Y,G,D,G,G,S,xT,F,Q,S,T,T,G,H,, +,,sp|P07737|PROF1_HUMAN,,S,T,G,G,A,P,xT,F,N,V,T,V,T,K,, +,,sp|P62191|PRS4_HUMAN,,A,V,A,N,Q,T,xS,A,T,F,L,R,,,, +,,sp|Q01469|FABP5_HUMAN,,,,,,,T,xT,Q,F,S,C,T,L,G,, +,,sp|P49321|NASP_HUMAN,E,P,E,V,N,G,G,xS,G,D,A,V,P,S,G,, +,,sp|Q02878|RL6_HUMAN,,,,,V,L,A,xT,V,T,K,P,V,G,G,, +,,sp|Q8IVH4|MMAA_HUMAN,,,,,,,,xS,T,F,I,E,Y,F,G,, +,,sp|Q9UHB9|SRP68_HUMAN,,,,,,F,E,xT,F,C,L,D,P,S,L,, +,,sp|Q93084|AT2A3_HUMAN; sp|P16615|AT2A2_HUMAN,,,,,,T,G,xT,L,T,T,N,Q,M,S,, +,,sp|Q15942|ZYX_HUMAN,,,,,,,,xS,P,G,A,P,G,P,L,, +,,sp|Q01469|FABP5_HUMAN,,,,,,T,Q,xT,V,C,N,F,T,D,G,, +,,sp|P11021|BIP_HUMAN,,V,T,H,A,V,V,xT,V,P,A,Y,F,N,D,, +,,sp|O15530|PDPK1_HUMAN,Q,G,P,A,M,D,G,xT,A,A,E,P,R,P,G,, +,,sp|Q9H0L4|CSTFT_HUMAN,,,,,,G,G,xT,L,L,S,V,T,G,E,, +,,sp|O00264|PGRC1_HUMAN; sp|O15173|PGRC2_HUMAN,,,,,G,L,A,xT,F,C,L,D,K,,,, +,,sp|O75937|DNJC8_HUMAN,,,,,,,,xT,F,L,R,P,P,K,,, +,,sp|O15530|PDPK1_HUMAN,,,T,Q,T,E,S,xS,T,P,P,G,I,P,G,, +,,sp|P14625|ENPL_HUMAN,P,E,E,T,A,E,D,xT,T,E,D,T,E,Q,D,, +,,sp|O14672|ADA10_HUMAN,,,,,,G,G,xT,F,Y,V,E,P,A,E,, +,,sp|O15530|PDPK1_HUMAN,,A,N,S,F,V,G,xT,A,Q,Y,V,S,P,E,, +,,sp|P23246|SFPQ_HUMAN,,,F,A,Q,H,G,xT,F,E,Y,E,Y,S,Q,, +,,sp|P13639|EF2_HUMAN,,,,,,,S,xT,L,T,D,S,L,V,C,, +,,sp|O94826|TOM70_HUMAN,,,,L,R,P,E,xS,A,L,A,Q,A,Q,K,, +,,sp|P51570|GALK1_HUMAN,E,H,Y,G,G,T,A,xT,F,Y,L,S,Q,A,A,, +,,sp|P25205|MCM3_HUMAN,,G,G,Y,T,S,G,xT,F,R,,,,,,, +,,sp|Q8ND56|LS14A_HUMAN,,,,,,,,xS,P,V,S,T,R,P,L,, +,,sp|P29401|TKT_HUMAN,,,,,,N,S,xT,F,S,E,I,F,K,K,, +,,sp|Q99832|TCPH_HUMAN,,,,,,,,xT,F,S,Y,A,G,F,E,, +,,sp|O95433|AHSA1_HUMAN,,,,,,,E,xT,F,L,T,S,P,E,E,, +,,sp|Q00610|CLH1_HUMAN,,,,,L,A,S,xT,L,V,H,L,G,E,Y,, +,,sp|P53597|SUCA_HUMAN,,,,,G,G,Q,xT,H,L,G,L,P,V,F,, +,,sp|Q00610|CLH1_HUMAN,,,,,,L,A,xS,T,L,V,H,L,G,E,, +,,sp|P49821|NDUV1_HUMAN,,,,,,G,G,xT,W,F,A,G,F,G,R,, +,,sp|P56556|NDUA6_HUMAN,,Q,A,T,S,T,A,xS,T,F,V,K,P,I,F,, +,,sp|Q8NF37|PCAT1_HUMAN,,,,,,,I,xT,F,A,D,F,H,R,,, +,,sp|O15530|PDPK1_HUMAN,Q,G,P,A,M,D,G,xT,A,A,E,P,R,,,, +,,sp|P06744|G6PI_HUMAN,,,,,,T,F,xT,T,Q,E,T,I,T,N,, +,,sp|C9JLW8|MCRI1_HUMAN,,,,S,P,P,S,xS,S,E,I,F,T,P,A,, +,,sp|Q99829|CPNE1_HUMAN,,,,,,,G,xT,I,T,V,S,A,Q,E,, +,,sp|O15530|PDPK1_HUMAN,,,,,,,,xT,F,F,V,H,T,P,N,, +,,sp|P30041|PRDX6_HUMAN,,,,,,V,A,xT,P,V,D,W,K,,,, +,,sp|P54578|UBP14_HUMAN,,,,,,G,G,xT,L,K,D,D,D,W,G,, +,,sp|Q6UWD8|CP054_HUMAN,,,,Q,R,P,G,xS,P,D,P,E,W,G,L,, +,,sp|Q01469|FABP5_HUMAN,,,,,,,K,xT,Q,T,V,C,N,F,T,, +,,sp|Q16563|SYPL1_HUMAN,,,,T,V,T,A,xT,F,G,Y,P,F,R,,, +,,sp|P08567|PLEK_HUMAN,,,,,,,G,xS,T,L,T,S,P,C,Q,, +,,sp|P28070|PSB4_HUMAN,,,,V,N,N,S,xT,M,L,G,A,S,G,D,, +,,sp|Q69YN4|VIR_HUMAN,Q,N,T,S,R,P,P,xS,M,H,V,D,D,F,V,, +,,sp|P25098|ARBK1_HUMAN,,,,,,,,xS,P,V,V,E,L,S,K,, +,,sp|Q86U90|YRDC_HUMAN,,,L,F,R,P,P,xS,P,A,P,A,A,P,G,, +,,sp|Q12905|ILF2_HUMAN,P,Q,G,E,E,E,E,xS,M,E,T,Q,E,,,, +,,sp|Q9UQ35|SRRM2_HUMAN,S,E,P,G,T,T,S,xT,Q,R,P,S,S,P,E,, +,,sp|P63010|AP2B1_HUMAN,,,,G,L,E,I,xS,G,T,F,T,H,R,,, +,,sp|P14625|ENPL_HUMAN,A,E,D,T,T,E,D,xT,E,Q,D,E,D,E,E,, +,,sp|O00541|PESC_HUMAN,,,,,,Y,P,xT,F,I,D,A,L,R,,, +,,sp|Q71DI3|H32_HUMAN; sp|P84243|H33_HUMAN; sp|P68431|H31_HUMAN; sp|Q16695|H31T_HUMAN; tr|Q5TEC6|Q5TEC6_HUMAN; sp|Q6NXT2|H3C_HUMAN,,,,Y,R,P,G,xT,V,A,L,R,,,,, +,,sp|P12956|XRCC6_HUMAN,,,,,,L,G,xS,L,V,D,E,F,K,,, +,,sp|Q9Y617|SERC_HUMAN,,,,,,F,G,xT,I,N,I,V,H,P,K,, +,,sp|P60709|ACTB_HUMAN,,,,,W,H,H,xT,F,Y,N,E,L,R,,, +,,sp|O94903|PLPHP_HUMAN,,,,,I,G,S,xT,I,F,G,E,R,,,, +,,sp|P32519|ELF1_HUMAN,T,K,P,P,R,P,D,xS,P,A,T,T,P,N,I,, +,,sp|Q9NVI7|ATD3A_HUMAN; sp|Q5T9A4|ATD3B_HUMAN,,,,,T,A,G,xT,L,F,G,E,G,F,R,, +,,sp|Q6L8Q7|PDE12_HUMAN,,Q,H,E,G,L,A,xT,F,Y,R,,,,,, +,,sp|Q9H0D6|XRN2_HUMAN,,,,,K,Y,P,xS,I,I,V,N,C,V,E,, +,,sp|Q9NZL9|MAT2B_HUMAN,,,,,,,G,xT,F,H,W,S,G,N,E,, +,,sp|P15498|VAV_HUMAN,,,,,,,G,xT,F,Y,Q,G,Y,R,,, +,,sp|Q92841|DDX17_HUMAN,,,,G,T,A,Y,xT,F,F,T,P,G,N,L,, +,,sp|Q2KHR2|RFX7_HUMAN,,,,,S,P,T,xT,V,L,F,T,S,S,P,, +,,sp|P52701|MSH6_HUMAN,,,,,,Q,S,xT,L,Y,S,F,F,P,K,, +,,sp|P26373|RL13_HUMAN,,,,,,V,A,xT,W,F,N,Q,P,A,R,, +,,sp|P62750|RL23A_HUMAN,,,,,,V,N,xT,L,I,R,P,D,G,E,, +,,sp|P11940|PABP1_HUMAN,,,,,A,L,D,xT,M,N,F,D,V,I,K,, +,,sp|Q00839|HNRPU_HUMAN,,,,,,,,xS,S,G,P,T,S,L,F,, +,,sp|P53396|ACLY_HUMAN,,,L,Y,R,P,G,xS,V,A,Y,V,S,R,,, +,,sp|P31146|COR1A_HUMAN,,,,,,K,G,xT,V,V,A,E,K,,,, +,,sp|Q8N6L1|KTAP2_HUMAN,,,,,,I,S,xS,T,L,Y,Q,A,A,A,, +,,sp|P68104|EF1A1_HUMAN; sp|Q5VTE0|EF1A3_HUMAN,,,,,S,T,T,xT,G,H,L,I,Y,K,,, +,,sp|Q14181|DPOA2_HUMAN,,,G,Q,V,G,G,xT,F,A,R,,,,,, +,,sp|P13667|PDIA4_HUMAN,,,V,E,G,F,P,xT,I,Y,F,A,P,S,G,, +,,sp|O00148|DX39A_HUMAN; sp|Q13838|DX39B_HUMAN,,,,G,L,A,I,xT,F,V,S,D,E,N,D,, +,,sp|P40227|TCPZ_HUMAN,,,,,,,H,xT,L,T,Q,I,K,,,, +,,sp|P53396|ACLY_HUMAN,,,,,,G,V,xT,I,I,G,P,A,T,V,, +,,sp|P06733|ENOA_HUMAN,,,,,,,,xT,I,A,P,A,L,V,S,, +,,sp|Q9BZK7|TBL1R_HUMAN; sp|Q9BQ87|TBL1Y_HUMAN; sp|O60907|TBL1X_HUMAN,,,,,,,,xT,T,I,I,W,D,A,H,, +,,sp|Q01469|FABP5_HUMAN,,,,,,,,xT,T,Q,F,S,C,T,L,, +,,sp|P05455|LA_HUMAN,,,,,,F,A,xS,D,D,E,H,D,E,H,, +,,sp|P48735|IDHP_HUMAN,,,N,I,L,G,G,xT,V,F,R,,,,,, +,,sp|O15530|PDPK1_HUMAN,,,,,,A,N,xS,F,V,G,T,A,Q,Y,, +,,sp|O43414|ERI3_HUMAN,,,,,,A,Y,xS,F,A,M,G,C,W,P,, +,,sp|Q9HB71|CYBP_HUMAN,,,,,,T,D,xT,V,L,I,L,C,R,,, +,,sp|P14625|ENPL_HUMAN,E,E,T,A,E,D,T,xT,E,D,T,E,Q,D,E,, +,,sp|P07437|TBB5_HUMAN; sp|P68371|TBB4B_HUMAN,,,,,I,M,N,xT,F,S,V,V,P,S,P,, +,,sp|P49368|TCPG_HUMAN,,,,,,A,M,xT,G,V,E,Q,W,P,Y,, +,,sp|Q9NR30|DDX21_HUMAN,,,,,,,,xT,F,H,H,V,Y,S,G,, +,,sp|P09211|GSTP1_HUMAN,,,,,P,P,Y,xT,V,V,Y,F,P,V,R,, +,,sp|Q9HCC0|MCCB_HUMAN,,,,,,,,xT,F,Y,N,Q,A,I,M,, +,,sp|Q8IVH4|MMAA_HUMAN,,,,,,,S,xT,F,I,E,Y,F,G,K,, +,,sp|P15880|RS2_HUMAN,,,,,,G,C,xT,A,T,L,G,N,F,A,, +,,sp|P19338|NUCL_HUMAN,,,,V,A,V,A,xT,P,A,K,,,,,, +,,sp|Q9UQ35|SRRM2_HUMAN,,,,,,,,xS,P,S,V,S,S,P,E,, +,,sp|Q96CW1|AP2M1_HUMAN,,,,,,,,xT,F,I,T,Q,Q,G,I,, +,,sp|Q92769|HDAC2_HUMAN,I,A,C,D,E,E,F,xS,D,S,E,D,E,G,E,, +,,sp|Q13126|MTAP_HUMAN,,T,T,M,R,P,Q,xS,F,Y,D,G,S,H,S,, +,,sp|O43175|SERA_HUMAN,,,,,,,G,xT,I,Q,V,I,T,Q,G,, +,,sp|P50452|SPB8_HUMAN; sp|P35237|SPB6_HUMAN,,,,,,T,G,xT,Q,Y,L,L,R,,,, +,,sp|P48444|COPD_HUMAN,,,,,,Q,H,xT,F,V,E,T,E,S,V,, +,,sp|P00558|PGK1_HUMAN,T,G,Q,A,T,V,A,xS,G,I,P,A,G,W,M,, +,,sp|P13639|EF2_HUMAN,,,,,,,,xT,F,C,Q,L,I,L,D,, +,,sp|P62191|PRS4_HUMAN,V,A,N,Q,T,S,A,xT,F,L,R,,,,,, +,,sp|P22681|CBL_HUMAN,,,V,E,R,P,P,xS,P,F,S,M,A,P,Q,, +,,sp|P19338|NUCL_HUMAN,D,D,D,E,E,D,D,xS,E,E,E,A,M,E,T,, +,,sp|P60709|ACTB_HUMAN,I,T,A,L,A,P,S,xT,M,K,,,,,,, +,,sp|Q15084|PDIA6_HUMAN,,,,,,,G,xS,F,S,E,Q,G,I,N,, +,,sp|P40939|ECHA_HUMAN,,,,,,D,A,xT,L,T,A,L,D,R,,, +,,sp|P39656|OST48_HUMAN,,,,,,A,P,xT,I,V,G,K,,,,, +,,sp|Q92900|RENT1_HUMAN,T,V,L,Q,R,P,L,xS,L,I,Q,G,P,P,G,, +,,sp|Q02790|FKBP4_HUMAN,,,,,G,E,H,xS,I,V,Y,L,K,P,S,, +,,sp|Q9Y5B9|SP16H_HUMAN,I,F,P,N,P,E,A,xT,F,V,K,,,,,, +,,sp|Q99832|TCPH_HUMAN,,,,,,T,F,xS,Y,A,G,F,E,M,Q,, +,,sp|P50995|ANX11_HUMAN,,,,,,,G,xT,I,T,D,A,P,G,F,, +,,sp|O15511|ARPC5_HUMAN,L,A,A,G,G,V,G,xS,I,V,R,,,,,, +,,sp|P06744|G6PI_HUMAN,,,,,,,,xT,F,T,T,Q,E,T,I,, +,,sp|P49721|PSB2_HUMAN,,,,Y,Y,T,P,xT,I,S,R,,,,,, +,,sp|P31948|STIP1_HUMAN,,,,,,,,xT,L,L,S,D,P,T,Y,, +,,sp|P50991|TCPD_HUMAN,,,,G,I,H,P,xT,I,I,S,E,S,F,Q,, +,,sp|Q99460|PSMD1_HUMAN,,,S,N,C,K,P,xS,T,F,A,Y,P,A,P,, +,,sp|Q92878|RAD50_HUMAN,,,,,,G,N,xT,F,V,H,D,P,K,,, +,,sp|P13639|EF2_HUMAN,,,,,,,,xT,G,T,I,T,T,F,E,, +,,sp|P40926|MDHM_HUMAN,,,,,,A,N,xT,F,V,A,E,L,K,,, +,,sp|P62917|RL8_HUMAN,,A,S,G,N,Y,A,xT,V,I,S,H,N,P,E,, +,,sp|P29350|PTN6_HUMAN,,,,,,D,G,xT,I,I,H,L,K,,,, +,,sp|P52272|HNRPM_HUMAN,,,G,N,F,G,G,xS,F,A,G,S,F,G,G,, +,,sp|P14625|ENPL_HUMAN,,,,,,G,T,xT,I,T,L,V,L,K,,, +,,sp|O15530|PDPK1_HUMAN,,T,Q,T,E,S,S,xT,P,P,G,I,P,G,G,, +,,sp|P37268|FDFT_HUMAN,,,,,,Y,Q,xT,V,I,A,D,I,C,R,, +,,sp|P37802|TAGL2_HUMAN,G,A,S,Q,A,G,M,xT,G,Y,G,M,P,R,,, +,,sp|Q01130|SRSF2_HUMAN,,,,,,,,xS,R,S,P,P,P,V,S,, +,,sp|Q9BY44|EIF2A_HUMAN,,,,,,D,G,xT,L,F,A,W,G,N,G,, +,,sp|P06733|ENOA_HUMAN,A,A,V,P,S,G,A,xS,T,G,I,Y,E,A,L,, +,,sp|P07437|TBB5_HUMAN,A,V,T,F,I,G,N,xS,T,A,I,Q,E,L,F,, +,,sp|P04406|G3P_HUMAN,,V,P,T,A,N,V,xS,V,V,D,L,T,C,R,, +,,sp|Q16666|IF16_HUMAN,,,,,,,,xT,T,I,Y,E,I,Q,D,, +,,sp|Q13126|MTAP_HUMAN,,,,,,,G,xT,M,V,T,I,E,G,P,, +,,sp|P07900|HS90A_HUMAN,P,E,I,E,D,V,G,xS,D,E,E,E,E,K,K,, +,,sp|O43491|E41L2_HUMAN,,V,C,V,E,H,H,xT,F,Y,R,,,,,, +,,sp|P19338|NUCL_HUMAN,A,A,A,A,A,P,A,xS,E,D,E,D,D,E,D,, +,,sp|P07737|PROF1_HUMAN,,,,,,,,xS,S,F,Y,V,N,G,L,, +,,sp|P78417|GSTO1_HUMAN,,V,P,S,L,V,G,xS,F,I,R,,,,,, +,,sp|Q14152|EIF3A_HUMAN,,,,,,L,A,xT,L,L,G,L,Q,A,P,, +,,sp|O00154|BACH_HUMAN,,,,,,,A,xT,L,W,Y,V,P,L,S,, +,,sp|P00558|PGK1_HUMAN,,,,,G,C,I,xT,I,I,G,G,G,D,T,, +,,sp|P78347|GTF2I_HUMAN,,,,,,S,P,xT,W,F,G,I,P,R,,, +,,sp|Q99832|TCPH_HUMAN,,,,,,,K,xT,F,S,Y,A,G,F,E,, +,,sp|P46940|IQGA1_HUMAN,,,,,,,A,xT,F,Y,G,E,Q,V,D,, +,,sp|P04406|G3P_HUMAN,,V,I,I,S,A,P,xS,A,D,A,P,M,F,V,, +,,sp|Q8NHW5|RLA0L_HUMAN; sp|P05388|RLA0_HUMAN,,,,,,,T,xS,F,F,Q,A,L,G,I,, +,,sp|P49411|EFTU_HUMAN,,,,,,,,xT,T,L,T,A,A,I,T,, +,,sp|O43159|RRP8_HUMAN,,,,Q,R,P,A,xS,L,V,V,A,D,F,G,, +,,sp|P35659|DEK_HUMAN,L,L,Y,N,R,P,G,xT,V,S,S,L,K,,,, +,,sp|Q00839|HNRPU_HUMAN,,,S,S,G,P,T,xS,L,F,A,V,T,V,A,, +,,sp|P08559|ODPA_HUMAN,,,,A,H,G,F,xT,F,T,R,,,,,, +,,sp|Q13547|HDAC1_HUMAN,I,A,C,E,E,E,F,xS,D,S,E,E,E,G,E,, +,,sp|P07437|TBB5_HUMAN,,,,,M,A,V,xT,F,I,G,N,S,T,A,, +,,sp|Q15084|PDIA6_HUMAN,V,D,A,D,K,H,H,xS,L,G,G,Q,Y,G,V,, +,,sp|O95433|AHSA1_HUMAN,,,,,,,Q,xT,F,G,Y,G,A,R,,, +,,sp|Q4KMQ1|TPRN_HUMAN,,,W,Q,R,P,S,xS,P,P,P,F,L,P,A,, +,,sp|P26641|EF1G_HUMAN,,,,,,A,G,xT,L,Y,T,Y,P,E,N,, +,,sp|P09874|PARP1_HUMAN,,,,,,V,G,xT,V,I,G,S,N,K,,, +,,sp|Q9NWH9|SLTM_HUMAN,,,,,,,,xS,P,G,H,M,V,I,L,, +,,sp|P30086|PEBP1_HUMAN,,,,N,R,P,T,xS,I,S,W,D,G,L,D,, +,,sp|Q15366|PCBP2_HUMAN,P,Y,R,P,K,P,S,xS,S,P,V,I,F,A,G,, +,,sp|O75436|VP26A_HUMAN,A,G,Y,D,P,T,P,xT,M,R,,,,,,, +,,sp|Q9BV79|MECR_HUMAN,,,,,,G,G,xT,M,V,T,Y,G,G,M,, +,,sp|O75643|U520_HUMAN,,,,,,S,P,xT,L,Y,G,I,S,H,D,, +,,sp|P06733|ENOA_HUMAN,,,,,G,N,P,xT,V,E,V,D,L,F,T,, +,,sp|P30041|PRDX6_HUMAN,,,,,R,V,A,xT,P,V,D,W,K,,,, +,,sp|Q9BVG9|PTSS2_HUMAN,A,G,G,P,R,P,E,xS,P,V,P,A,G,R,,, +,,sp|Q9Y6X4|F169A_HUMAN,,,,,R,P,M,xS,G,E,Y,G,P,A,S,, +,,sp|P22626|ROA2_HUMAN,,,,,,I,D,xT,I,E,I,I,T,D,R,, +,,sp|O15530|PDPK1_HUMAN,,,I,L,G,E,G,xS,F,S,T,V,V,L,A,, +,,sp|Q7L2R6|ZN765_HUMAN,,,,,,,,xS,K,L,Q,I,H,R,,, +,,sp|P62937|PPIA_HUMAN,,,,,V,N,P,xT,V,F,F,D,I,A,V,, +,,sp|Q9NYF8|BCLF1_HUMAN,,,,,,,,xS,P,H,S,P,S,P,I,, +,,sp|P20042|IF2B_HUMAN,,,,,,,,xT,S,F,V,N,F,T,D,, +,,sp|Q2KHR2|RFX7_HUMAN,,,,,,S,P,xT,T,V,L,F,T,S,S,, +,,sp|Q15365|PCBP1_HUMAN,,,,,,A,I,xT,I,A,G,V,P,Q,S,, +,,sp|Q8NBS9|TXND5_HUMAN,,,,,G,Y,P,xT,L,L,W,F,R,,,, +,,sp|Q8IYB3|SRRM1_HUMAN,,,,,,,,xS,P,S,P,A,P,P,P,, +,,sp|Q07020|RL18_HUMAN,,T,A,V,V,V,G,xT,I,T,D,D,V,R,,, +,,sp|Q13200|PSMD2_HUMAN,,,,,G,T,L,xT,L,C,P,Y,H,S,D,, +,,sp|P51610|HCFC1_HUMAN,G,A,P,G,Q,P,G,xT,I,L,R,,,,,, +,,sp|Q6NYC8|PPR18_HUMAN,,,,,S,G,H,xT,F,T,V,N,P,R,,, +,,sp|Q15029|U5S1_HUMAN,,,,,,T,A,xT,I,T,E,P,R,,,, +,,sp|Q8IYD1|ERF3B_HUMAN; sp|P15170|ERF3A_HUMAN,,,,,T,A,G,xT,I,C,L,E,T,F,K,, +,,sp|P56556|NDUA6_HUMAN,,,,,Q,A,T,xS,T,A,S,T,F,V,K,, +,,sp|P07737|PROF1_HUMAN,,,,,,,,xT,L,V,L,L,M,G,K,, +,,sp|Q8NC51|PAIRB_HUMAN,,,,,,,,xS,S,F,S,H,Y,S,G,, +,,sp|Q6NYC8|PPR18_HUMAN,,,,,,,,xS,G,H,T,F,T,V,N,, +,,sp|Q8NBQ5|DHB11_HUMAN,,,,,,V,H,xT,F,V,V,D,C,S,N,, +,,sp|P84090|ERH_HUMAN,,,,,,S,H,xT,I,L,L,V,Q,P,T,, +,,sp|P04406|G3P_HUMAN,,,,,V,I,I,xS,A,P,S,A,D,A,P,, +,,sp|Q9Y5K5|UCHL5_HUMAN,,,,,,L,D,xT,I,F,F,A,K,,,, +,,sp|P49585|PCY1A_HUMAN,,,,E,R,S,P,xS,P,S,F,R,,,,, +,,sp|Q68EM7|RHG17_HUMAN,,,,K,R,P,A,xS,M,A,V,M,E,G,D,, +,,sp|Q96I25|SPF45_HUMAN,,,S,P,T,G,P,xS,N,S,F,L,A,N,M,, +,,sp|O75436|VP26A_HUMAN,F,L,A,G,Y,D,P,xT,P,T,M,R,,,,, +,,sp|P53396|ACLY_HUMAN,,,,,,S,T,xT,L,F,S,R,,,,, +,,sp|P26641|EF1G_HUMAN,,,,,,,,xS,T,F,V,L,D,E,F,, +,,sp|O15530|PDPK1_HUMAN,L,G,E,G,S,F,S,xT,V,V,L,A,R,,,, +,,sp|P20292|AL5AP_HUMAN,,,,,,T,G,xT,L,A,F,E,R,,,, +,,sp|Q99460|PSMD1_HUMAN,,S,N,C,K,P,S,xT,F,A,Y,P,A,P,L,, +,,sp|P68363|TBA1B_HUMAN; sp|Q71U36|TBA1A_HUMAN,G,G,D,D,S,F,N,xT,F,F,S,E,T,G,A,, +,,sp|Q01469|FABP5_HUMAN,,,,,K,T,Q,xT,V,C,N,F,T,D,G,, +,,sp|P04040|CATA_HUMAN,,,,N,A,I,H,xT,F,V,Q,S,G,S,H,, +,,sp|P60709|ACTB_HUMAN,,,,I,W,H,H,xT,F,Y,N,E,L,R,,, +,,sp|P60709|ACTB_HUMAN,,,,,,,H,xT,F,Y,N,E,L,R,,, +,,sp|Q00839|HNRPU_HUMAN,,,,,,L,N,xT,L,L,Q,R,,,,, +,,sp|Q93084|AT2A3_HUMAN; sp|P16615|AT2A2_HUMAN,,,,,,,,xT,G,T,L,T,T,N,Q,, +,,sp|P52272|HNRPM_HUMAN,,,,,L,G,S,xT,V,F,V,A,N,L,D,, +,,sp|Q9UQ35|SRRM2_HUMAN,F,S,E,P,G,T,T,xS,T,Q,R,P,S,S,P,, +,,sp|Q9BRB3|PIGQ_HUMAN,,,,,,G,G,xT,F,W,S,C,E,A,T,, +,,sp|Q96A35|RM24_HUMAN,,,,,,,G,xT,M,I,P,S,E,A,P,, +,,sp|Q07020|RL18_HUMAN,,,,,T,N,S,xT,F,N,Q,V,V,L,K,, +,,sp|P22626|ROA2_HUMAN,,,G,F,G,F,V,xT,F,D,D,H,D,P,V,, +,,sp|P23246|SFPQ_HUMAN,,,,,,F,A,xT,H,A,A,A,L,S,V,, +,,sp|Q15366|PCBP2_HUMAN,I,P,Y,R,P,K,P,xS,S,S,P,V,I,F,A,, +,,sp|P26641|EF1G_HUMAN,,,,,A,A,G,xT,L,Y,T,Y,P,E,N,, +,,sp|P11142|HSP7C_HUMAN,,,,,T,T,P,xS,Y,V,A,F,T,D,T,, +,,sp|P35269|T2FA_HUMAN,,G,N,S,R,P,G,xT,P,S,A,E,G,G,S,, +,,sp|P49327|FAS_HUMAN,,,,S,F,Y,G,xS,T,L,F,L,C,R,,, +,,sp|P07686|HEXB_HUMAN,,,,L,A,P,G,xT,I,V,E,V,W,K,,, +,,sp|P07814|SYEP_HUMAN,,,A,I,Q,G,G,xT,S,H,H,L,G,Q,N,, +,,sp|Q9Y277|VDAC3_HUMAN,,V,C,N,Y,G,L,xT,F,T,Q,K,,,,, +,,sp|P62805|H4_HUMAN,,,,,D,A,V,xT,Y,T,E,H,A,K,,, +,,sp|P21796|VDAC1_HUMAN,,,,,,,L,xT,F,D,S,S,F,S,P,, +,,sp|Q86VP6|CAND1_HUMAN,,,,,,A,L,xT,L,I,A,G,S,P,L,, +,,sp|P04080|CYTB_HUMAN,,S,Q,V,V,A,G,xT,N,Y,F,I,K,,,, +,,sp|P06748|NPM_HUMAN,D,E,N,E,H,Q,L,xS,L,R,,,,,,, +,,sp|Q96C86|DCPS_HUMAN,,,,,,,,xT,T,V,V,Y,P,A,T,, +,,sp|P61604|CH10_HUMAN,,,,V,L,Q,A,xT,V,V,A,V,G,S,G,, +,,sp|O00461|GOLI4_HUMAN,Y,G,E,N,D,E,N,xT,D,D,K,N,N,D,G,, +,,sp|P19338|NUCL_HUMAN,,,,,,S,I,xS,L,Y,Y,T,G,E,K,, +,,sp|P30086|PEBP1_HUMAN,,,,,,L,Y,xT,L,V,L,T,D,P,D,, +,,sp|O00299|CLIC1_HUMAN,,,,,,G,V,xT,F,N,V,T,T,V,D,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/SBF1.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,36 @@ +Amino Acids,sp|P47756|CAPZB_HUMAN,sp|P49189|AL9A1_HUMAN,sp|P19338|NUCL_HUMAN,sp|O00567|NOP56_HUMAN,sp|Q9UQ35|SRRM2_HUMAN,sp|P13639|EF2_HUMAN,sp|P60709|ACTB_HUMAN,sp|P63261|ACTG_HUMAN,sp|P11021|BIP_HUMAN,sp|Q16698|DECR_HUMAN,sp|Q9HD20|AT131_HUMAN,sp|Q9UQB8|BAIP2_HUMAN,sp|P11142|HSP7C_HUMAN,sp|O00541|PESC_HUMAN,sp|P08238|HS90B_HUMAN,sp|Q06830|PRDX1_HUMAN,sp|P35249|RFC4_HUMAN,sp|Q14974|IMB1_HUMAN,sp|O15530|PDPK1_HUMAN,sp|Q14258|TRI25_HUMAN,sp|Q53H96|P5CR3_HUMAN,sp|Q9Y5S9|RBM8A_HUMAN,sp|P30086|PEBP1_HUMAN,sp|P62081|RS7_HUMAN,sp|Q92900|RENT1_HUMAN,sp|P05455|LA_HUMAN,sp|Q32P44|EMAL3_HUMAN,sp|P41252|SYIC_HUMAN,sp|P48047|ATPO_HUMAN,tr|H7C0C1|H7C0C1_HUMAN,sp|P26373|RL13_HUMAN,sp|Q9Y3D7|TIM16_HUMAN,sp|P00338|LDHA_HUMAN,sp|P55884|EIF3B_HUMAN,sp|Q16658|FSCN1_HUMAN,sp|Q9HC35|EMAL4_HUMAN,sp|P09211|GSTP1_HUMAN,sp|P04083|ANXA1_HUMAN,sp|P29590|PML_HUMAN,sp|P07900|HS90A_HUMAN,sp|P31943|HNRH1_HUMAN,sp|P07737|PROF1_HUMAN,sp|P49321|NASP_HUMAN,sp|P49736|MCM2_HUMAN,sp|P14625|ENPL_HUMAN,sp|Q9BQE3|TBA1C_HUMAN,sp|P68363|TBA1B_HUMAN,sp|Q71U36|TBA1A_HUMAN,sp|P62191|PRS4_HUMAN,sp|Q01469|FABP5_HUMAN,sp|Q14554|PDIA5_HUMAN,sp|Q9Y266|NUDC_HUMAN,sp|P06748|NPM_HUMAN,sp|O75534|CSDE1_HUMAN,sp|Q02878|RL6_HUMAN,sp|Q8NHW5|RLA0L_HUMAN,sp|P05388|RLA0_HUMAN,sp|Q7Z5L9|I2BP2_HUMAN,sp|Q00613|HSF1_HUMAN,sp|P47712|PA24A_HUMAN,sp|Q8IVH4|MMAA_HUMAN,sp|P53597|SUCA_HUMAN,sp|Q15942|ZYX_HUMAN,sp|Q9H0L4|CSTFT_HUMAN,sp|P33240|CSTF2_HUMAN,sp|O75937|DNJC8_HUMAN,sp|Q96A26|F162A_HUMAN,sp|P51570|GALK1_HUMAN,sp|P30101|PDIA3_HUMAN,sp|Q16851|UGPA_HUMAN,sp|P23193|TCEA1_HUMAN,sp|Q15560|TCEA2_HUMAN,sp|Q9H6F5|CCD86_HUMAN,sp|O14672|ADA10_HUMAN,sp|Q5H9R7|PP6R3_HUMAN,sp|P49411|EFTU_HUMAN,sp|P23246|SFPQ_HUMAN,sp|Q4KMQ1|TPRN_HUMAN,sp|O94826|TOM70_HUMAN,sp|O75995|SASH3_HUMAN,sp|Q13200|PSMD2_HUMAN,sp|O43776|SYNC_HUMAN,sp|Q9HCC0|MCCB_HUMAN,sp|P42166|LAP2A_HUMAN,sp|O43760|SNG2_HUMAN,sp|Q8ND56|LS14A_HUMAN,sp|P29401|TKT_HUMAN,sp|Q99832|TCPH_HUMAN,sp|P62701|RS4X_HUMAN,sp|Q8TD47|RS4Y2_HUMAN,sp|O95433|AHSA1_HUMAN,sp|Q00610|CLH1_HUMAN,sp|Q6UN15|FIP1_HUMAN,sp|P49821|NDUV1_HUMAN,sp|P0DP23|CALM1_HUMAN,sp|P0DP25|CALM3_HUMAN,sp|P0DP24|CALM2_HUMAN,sp|P40926|MDHM_HUMAN,sp|P56556|NDUA6_HUMAN,sp|P00387|NB5R3_HUMAN,sp|P40123|CAP2_HUMAN,sp|Q01518|CAP1_HUMAN,sp|Q8NF37|PCAT1_HUMAN,sp|C9JLW8|MCRI1_HUMAN,sp|Q99829|CPNE1_HUMAN,sp|Q9NYF8|BCLF1_HUMAN,sp|Q8IYB3|SRRM1_HUMAN,sp|P62942|FKB1A_HUMAN,sp|P30041|PRDX6_HUMAN,sp|P54578|UBP14_HUMAN,sp|O60934|NBN_HUMAN,sp|O43660|PLRG1_HUMAN,sp|Q6UWD8|CP054_HUMAN,sp|Q5VTE0|EF1A3_HUMAN,sp|P68104|EF1A1_HUMAN,sp|P63244|RACK1_HUMAN,sp|Q9BZK7|TBL1R_HUMAN,sp|O60907|TBL1X_HUMAN,sp|Q9BQ87|TBL1Y_HUMAN,sp|Q16563|SYPL1_HUMAN,sp|P37198|NUP62_HUMAN,sp|P08567|PLEK_HUMAN,sp|Q6ZT62|BGIN_HUMAN,sp|Q9Y3L3|3BP1_HUMAN,sp|P25098|ARBK1_HUMAN,sp|Q86U90|YRDC_HUMAN,sp|P26641|EF1G_HUMAN,sp|Q92974|ARHG2_HUMAN,sp|P63010|AP2B1_HUMAN,sp|Q9NP66|HM20A_HUMAN,sp|Q92841|DDX17_HUMAN,sp|Q7KZF4|SND1_HUMAN,sp|P12956|XRCC6_HUMAN,sp|Q9Y617|SERC_HUMAN,sp|O94903|PLPHP_HUMAN,sp|P32519|ELF1_HUMAN,sp|Q9NVI7|ATD3A_HUMAN,sp|Q5T9A4|ATD3B_HUMAN,sp|P09651|ROA1_HUMAN,sp|Q32P51|RA1L2_HUMAN,sp|P51991|ROA3_HUMAN,sp|P55263|ADK_HUMAN,sp|Q96FV9|THOC1_HUMAN,sp|Q6L8Q7|PDE12_HUMAN,sp|Q9H0D6|XRN2_HUMAN,sp|Q92499|DDX1_HUMAN,sp|Q9NZL9|MAT2B_HUMAN,sp|Q01082|SPTB2_HUMAN,sp|Q2KHR2|RFX7_HUMAN,sp|P52701|MSH6_HUMAN,sp|P17947|SPI1_HUMAN,sp|P53396|ACLY_HUMAN,sp|P31146|COR1A_HUMAN,sp|P63167|DYL1_HUMAN,sp|Q96FJ2|DYL2_HUMAN,sp|Q14181|DPOA2_HUMAN,sp|Q96JM3|CHAP1_HUMAN,sp|Q969T9|WBP2_HUMAN,sp|P13667|PDIA4_HUMAN,sp|P07195|LDHB_HUMAN,sp|Q9Y678|COPG1_HUMAN,sp|O00148|DX39A_HUMAN,sp|Q13838|DX39B_HUMAN,sp|P07437|TBB5_HUMAN,sp|P06733|ENOA_HUMAN,sp|P48735|IDHP_HUMAN,sp|Q14161|GIT2_HUMAN,sp|P28066|PSA5_HUMAN,sp|Q9HB71|CYBP_HUMAN,sp|Q15084|PDIA6_HUMAN,sp|Q13509|TBB3_HUMAN,tr|A0A0B4J269|A0A0B4J269_HUMAN,sp|P49368|TCPG_HUMAN,sp|Q92608|DOCK2_HUMAN,sp|P62807|H2B1C_HUMAN,sp|O60814|H2B1K_HUMAN,sp|Q99880|H2B1L_HUMAN,sp|P58876|H2B1D_HUMAN,sp|Q93079|H2B1H_HUMAN,sp|Q5QNW6|H2B2F_HUMAN,sp|Q99877|H2B1N_HUMAN,sp|P57053|H2BFS_HUMAN,sp|Q99879|H2B1M_HUMAN,sp|Q9Y5B9|SP16H_HUMAN,sp|Q9NR30|DDX21_HUMAN,sp|P15880|RS2_HUMAN,sp|Q15019|SEPT2_HUMAN,sp|Q15185|TEBP_HUMAN,sp|P25205|MCM3_HUMAN,sp|P38646|GRP75_HUMAN,sp|Q96CW1|AP2M1_HUMAN,sp|Q92769|HDAC2_HUMAN,sp|Q15370|ELOB_HUMAN,sp|Q13126|MTAP_HUMAN,sp|P50452|SPB8_HUMAN,sp|P35237|SPB6_HUMAN,sp|O95218|ZRAB2_HUMAN,sp|P22392|NDKB_HUMAN,sp|O00461|GOLI4_HUMAN,sp|P10809|CH60_HUMAN,sp|P00558|PGK1_HUMAN,sp|P48444|COPD_HUMAN,sp|P46776|RL27A_HUMAN,sp|P54105|ICLN_HUMAN,sp|P22681|CBL_HUMAN,sp|Q9UJ68|MSRA_HUMAN,sp|P25705|ATPA_HUMAN,sp|Q13616|CUL1_HUMAN,sp|Q16629|SRSF7_HUMAN,sp|P17480|UBF1_HUMAN,sp|P40939|ECHA_HUMAN,sp|Q02790|FKBP4_HUMAN,sp|Q16695|H31T_HUMAN,sp|P68431|H31_HUMAN,sp|P84243|H33_HUMAN,sp|Q6NXT2|H3C_HUMAN,sp|Q71DI3|H32_HUMAN,tr|Q5TEC6|Q5TEC6_HUMAN,sp|Q10567|AP1B1_HUMAN,sp|P17844|DDX5_HUMAN,sp|P50995|ANX11_HUMAN,sp|O15511|ARPC5_HUMAN,sp|P49721|PSB2_HUMAN,sp|P31948|STIP1_HUMAN,sp|Q9H1E3|NUCKS_HUMAN,sp|P11940|PABP1_HUMAN,sp|P50991|TCPD_HUMAN,sp|Q8TBC3|SHKB1_HUMAN,sp|Q99460|PSMD1_HUMAN,sp|Q92878|RAD50_HUMAN,sp|P62917|RL8_HUMAN,sp|P40763|STAT3_HUMAN,sp|Q8N8J7|F241A_HUMAN,sp|P29350|PTN6_HUMAN,sp|P52272|HNRPM_HUMAN,sp|P37268|FDFT_HUMAN,sp|Q14697|GANAB_HUMAN,sp|Q9BY44|EIF2A_HUMAN,sp|P04406|G3P_HUMAN,sp|Q16666|IF16_HUMAN,sp|P54886|P5CS_HUMAN,sp|P20042|IF2B_HUMAN,sp|Q92541|RTF1_HUMAN,sp|Q9NSD9|SYFB_HUMAN,sp|P23528|COF1_HUMAN,sp|Q14152|EIF3A_HUMAN,sp|Q13423|NNTM_HUMAN,sp|P46940|IQGA1_HUMAN,sp|O75746|CMC1_HUMAN,sp|Q9BT22|ALG1_HUMAN,sp|C9J202|AG1L2_HUMAN,sp|O43159|RRP8_HUMAN,sp|P08559|ODPA_HUMAN,sp|P47897|SYQ_HUMAN,sp|Q13547|HDAC1_HUMAN,sp|Q15366|PCBP2_HUMAN,sp|P50748|KNTC1_HUMAN,sp|P09429|HMGB1_HUMAN,sp|P26583|HMGB2_HUMAN,sp|P09874|PARP1_HUMAN,sp|Q9NWH9|SLTM_HUMAN,sp|O75643|U520_HUMAN,sp|P22626|ROA2_HUMAN,sp|P57764|GSDMD_HUMAN,sp|Q9Y6X4|F169A_HUMAN,sp|P18031|PTN1_HUMAN,sp|Q6ZSZ5|ARHGI_HUMAN,tr|A0A087WZG4|A0A087WZG4_HUMAN,sp|P62937|PPIA_HUMAN,sp|O75506|HSBP1_HUMAN,sp|P08236|BGLR_HUMAN,sp|Q15365|PCBP1_HUMAN,sp|P08865|RSSA_HUMAN,sp|Q07020|RL18_HUMAN,sp|P27824|CALX_HUMAN,sp|Q86YP4|P66A_HUMAN,sp|P98171|RHG04_HUMAN,sp|E9PAV3|NACAM_HUMAN,sp|Q6NYC8|PPR18_HUMAN,sp|Q8IYD1|ERF3B_HUMAN,sp|P15170|ERF3A_HUMAN,sp|P51858|HDGF_HUMAN,sp|Q8NBQ5|DHB11_HUMAN,sp|O95340|PAPS2_HUMAN,sp|O43252|PAPS1_HUMAN,sp|P37802|TAGL2_HUMAN,sp|P84090|ERH_HUMAN,sp|Q9Y5K5|UCHL5_HUMAN,sp|Q68EM7|RHG17_HUMAN,sp|P08621|RU17_HUMAN,sp|O00154|BACH_HUMAN,sp|P23786|CPT2_HUMAN,sp|P20292|AL5AP_HUMAN,sp|P35269|T2FA_HUMAN,sp|Q8IY67|RAVR1_HUMAN,sp|Q9UKW4|VAV3_HUMAN,sp|P04040|CATA_HUMAN,sp|Q00839|HNRPU_HUMAN,sp|P08183|MDR1_HUMAN,sp|P21439|MDR3_HUMAN,sp|Q9BRB3|PIGQ_HUMAN,sp|Q96A35|RM24_HUMAN,sp|P00352|AL1A1_HUMAN,sp|P0DMV8|HS71A_HUMAN,sp|P0DMV9|HS71B_HUMAN,sp|Q5TC12|ATPF1_HUMAN,sp|P35244|RFA3_HUMAN,sp|P49327|FAS_HUMAN,sp|Q96C86|DCPS_HUMAN,sp|P0DPI2|GAL3A_HUMAN,tr|A0A096LPI6|A0A096LPI6_HUMAN,sp|A0A0B4J2D5|GAL3B_HUMAN,sp|P21796|VDAC1_HUMAN,sp|Q86VP6|CAND1_HUMAN,sp|P78371|TCPB_HUMAN,sp|P04080|CYTB_HUMAN,sp|P16150|LEUK_HUMAN,sp|P61604|CH10_HUMAN,sp|Q96L21|RL10L_HUMAN,sp|P27635|RL10_HUMAN,sp|P45880|VDAC2_HUMAN,sp|P60174|TPIS_HUMAN,sp|O00299|CLIC1_HUMAN,sp|P30040|ERP29_HUMAN 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ST,34,53,74,81,814,85,51,51,77,49,145,83,82,50,82,22,47,92,70,83,34,13,24,20,137,32,138,151,34,47,19,11,38,86,71,164,19,41,113,85,53,21,100,99,104,52,52,51,47,21,48,33,36,88,30,38,37,84,95,103,52,45,65,61,50,23,23,47,50,67,46,43,43,94,149,42,60,88,50,60,95,56,49,124,27,72,74,55,27,27,46,149,97,50,16,16,16,46,14,29,67,67,60,18,65,193,190,12,23,66,119,81,30,51,52,61,81,100,88,37,135,38,95,107,63,33,51,136,104,51,88,97,71,37,29,113,64,68,54,46,37,35,90,79,79,74,30,268,304,194,31,124,61,8,8,96,139,27,59,39,123,38,35,57,44,53,131,35,32,49,59,101,66,217,22,21,23,23,22,22,23,21,21,116,100,35,30,18,108,83,51,47,17,43,45,51,90,12,42,59,41,67,12,34,139,31,66,92,52,94,86,46,16,15,16,17,16,16,112,68,57,18,18,38,40,69,77,113,103,145,19,98,8,74,46,50,108,77,42,131,98,37,102,61,19,107,134,161,74,46,29,54,38,79,47,67,291,16,21,127,158,236,37,66,115,51,189,146,19,13,80,60,38,23,48,116,121,487,76,82,49,23,41,61,51,17,12,30,128,33,46,91,22,78,69,85,49,67,157,153,82,22,57,75,75,33,10,314,29,27,27,27,48,177,61,13,112,9,14,13,54,30,25,24 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AAs,277,494,710,594,2752,858,375,375,654,335,1204,552,646,588,724,199,363,876,556,630,274,174,187,194,1129,408,896,1262,213,242,211,125,332,814,493,981,210,346,882,732,449,140,788,904,803,449,451,451,440,135,519,331,294,798,288,317,317,587,529,749,418,346,572,616,577,253,154,392,505,508,301,299,360,748,873,452,707,711,608,380,908,548,563,694,224,463,623,543,263,263,338,1675,594,464,149,149,149,338,128,301,477,475,534,97,537,920,904,108,224,494,754,514,224,462,462,317,514,577,522,259,522,350,677,701,689,279,437,986,937,347,729,910,609,370,275,619,634,648,372,320,378,362,657,609,950,740,334,2364,1363,1360,270,1101,461,89,89,598,812,261,645,334,874,427,428,444,434,452,759,241,228,440,450,797,545,1830,126,126,126,126,126,126,126,126,126,1047,783,293,361,160,808,679,435,488,118,283,374,376,330,152,696,573,417,511,148,237,906,235,553,776,238,764,763,459,136,136,136,135,136,136,949,614,505,151,201,543,243,636,539,707,953,1312,257,770,132,595,730,417,944,585,335,785,795,333,710,589,166,1382,1086,1657,678,464,215,456,390,775,482,365,2209,215,209,1014,1034,2136,353,484,670,435,1361,1122,165,76,651,356,295,188,592,633,946,2078,613,628,499,240,300,614,624,199,104,329,881,437,380,658,161,517,606,847,527,825,1280,1286,760,216,501,641,641,328,121,2511,337,268,279,268,283,1230,535,98,400,102,214,214,294,286,241,261
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all stuff/test-data/SBF2.csv Wed Jan 16 13:55:22 2019 -0500 @@ -0,0 +1,36 @@ +Amino Acids,sp|Q13283|G3BP1_HUMAN,sp|O43707|ACTN4_HUMAN,sp|P35609|ACTN2_HUMAN,sp|Q08043|ACTN3_HUMAN,sp|P12814|ACTN1_HUMAN,sp|P19338|NUCL_HUMAN,sp|Q15738|NSDHL_HUMAN,sp|P13639|EF2_HUMAN,sp|P60709|ACTB_HUMAN,sp|P63261|ACTG_HUMAN,sp|P11021|BIP_HUMAN,sp|Q9HD20|AT131_HUMAN,sp|Q9UQB8|BAIP2_HUMAN,sp|Q9UQ35|SRRM2_HUMAN,sp|Q06830|PRDX1_HUMAN,sp|Q9Y371|SHLB1_HUMAN,sp|P08238|HS90B_HUMAN,sp|Q14974|IMB1_HUMAN,sp|P09651|ROA1_HUMAN,sp|Q32P51|RA1L2_HUMAN,sp|O15530|PDPK1_HUMAN,sp|Q14258|TRI25_HUMAN,sp|Q9Y5S9|RBM8A_HUMAN,sp|P54136|SYRC_HUMAN,sp|P30086|PEBP1_HUMAN,sp|P22626|ROA2_HUMAN,sp|Q32P44|EMAL3_HUMAN,sp|Q8NBS9|TXND5_HUMAN,sp|P41252|SYIC_HUMAN,sp|Q96JH7|VCIP1_HUMAN,sp|P09211|GSTP1_HUMAN,sp|P04083|ANXA1_HUMAN,sp|P07195|LDHB_HUMAN,sp|P07900|HS90A_HUMAN,sp|P49321|NASP_HUMAN,sp|Q9BQE3|TBA1C_HUMAN,sp|P68363|TBA1B_HUMAN,sp|Q71U36|TBA1A_HUMAN,sp|P14625|ENPL_HUMAN,sp|Q14554|PDIA5_HUMAN,sp|Q15007|FL2D_HUMAN,sp|Q9Y266|NUDC_HUMAN,sp|P06748|NPM_HUMAN,sp|O14776|TCRG1_HUMAN,sp|O75534|CSDE1_HUMAN,sp|O15294|OGT1_HUMAN,sp|Q8NHW5|RLA0L_HUMAN,sp|P05388|RLA0_HUMAN,sp|Q9UKX7|NUP50_HUMAN,sp|O43312|MTSS1_HUMAN,sp|Q00613|HSF1_HUMAN,sp|P47712|PA24A_HUMAN,sp|P22314|UBA1_HUMAN,sp|P53597|SUCA_HUMAN,sp|O75746|CMC1_HUMAN,sp|Q96A26|F162A_HUMAN,sp|P51570|GALK1_HUMAN,sp|Q15005|SPCS2_HUMAN,sp|P30101|PDIA3_HUMAN,sp|P23193|TCEA1_HUMAN,sp|Q15560|TCEA2_HUMAN,sp|Q16851|UGPA_HUMAN,sp|P62995|TRA2B_HUMAN,sp|Q13596|SNX1_HUMAN,sp|Q4KMQ1|TPRN_HUMAN,sp|Q13200|PSMD2_HUMAN,sp|P42166|LAP2A_HUMAN,sp|O43776|SYNC_HUMAN,sp|Q9HCC0|MCCB_HUMAN,sp|O43760|SNG2_HUMAN,sp|P62701|RS4X_HUMAN,sp|Q8TD47|RS4Y2_HUMAN,sp|Q6UN15|FIP1_HUMAN,sp|P40926|MDHM_HUMAN,sp|P11142|HSP7C_HUMAN,sp|P0DMV8|HS71A_HUMAN,sp|P0DMV9|HS71B_HUMAN,sp|P00387|NB5R3_HUMAN,sp|P25789|PSA4_HUMAN,sp|P07737|PROF1_HUMAN,sp|Q9NYF8|BCLF1_HUMAN,sp|P49189|AL9A1_HUMAN,sp|P62942|FKB1A_HUMAN,sp|Q9Y277|VDAC3_HUMAN,sp|O75521|ECI2_HUMAN,sp|O60934|NBN_HUMAN,sp|P04075|ALDOA_HUMAN,sp|Q5VTE0|EF1A3_HUMAN,sp|P68104|EF1A1_HUMAN,sp|P63244|RACK1_HUMAN,sp|Q92900|RENT1_HUMAN,sp|Q9BZK7|TBL1R_HUMAN,sp|O60907|TBL1X_HUMAN,sp|Q9BQ87|TBL1Y_HUMAN,sp|Q14498|RBM39_HUMAN,sp|P37198|NUP62_HUMAN,sp|Q6ZT62|BGIN_HUMAN,sp|Q9Y3L3|3BP1_HUMAN,sp|Q9UPN3|MACF1_HUMAN,sp|P12955|PEPD_HUMAN,sp|P26641|EF1G_HUMAN,sp|Q92974|ARHG2_HUMAN,sp|Q9ULW0|TPX2_HUMAN,sp|Q9NP66|HM20A_HUMAN,sp|Q13177|PAK2_HUMAN,sp|Q92841|DDX17_HUMAN,sp|Q7KZF4|SND1_HUMAN,sp|P62987|RL40_HUMAN,sp|P0CG47|UBB_HUMAN,tr|A0A2R8Y422|A0A2R8Y422_HUMAN,sp|P0CG48|UBC_HUMAN,sp|P62979|RS27A_HUMAN,sp|P51991|ROA3_HUMAN,sp|P55263|ADK_HUMAN,sp|P17844|DDX5_HUMAN,sp|Q96FV9|THOC1_HUMAN,sp|Q92499|DDX1_HUMAN,sp|Q01082|SPTB2_HUMAN,sp|P12956|XRCC6_HUMAN,sp|C9JLW8|MCRI1_HUMAN,sp|P63167|DYL1_HUMAN,sp|Q96FJ2|DYL2_HUMAN,sp|Q9UGU5|HMGX4_HUMAN,sp|Q969T9|WBP2_HUMAN,sp|Q15181|IPYR_HUMAN,sp|Q9Y678|COPG1_HUMAN,sp|P07437|TBB5_HUMAN,sp|Q9NUL3|STAU2_HUMAN,sp|P24752|THIL_HUMAN,sp|P60900|PSA6_HUMAN,sp|P63010|AP2B1_HUMAN,sp|Q10567|AP1B1_HUMAN,sp|Q14161|GIT2_HUMAN,sp|Q15084|PDIA6_HUMAN,sp|Q92608|DOCK2_HUMAN,sp|Q99832|TCPH_HUMAN,sp|P53396|ACLY_HUMAN,sp|A0FGR8|ESYT2_HUMAN,sp|Q15019|SEPT2_HUMAN,sp|Q15185|TEBP_HUMAN,sp|P49407|ARRB1_HUMAN,sp|Q15370|ELOB_HUMAN,sp|O95218|ZRAB2_HUMAN,sp|P22392|NDKB_HUMAN,sp|O00461|GOLI4_HUMAN,sp|Q96I25|SPF45_HUMAN,sp|P10809|CH60_HUMAN,sp|O60506|HNRPQ_HUMAN,sp|O00148|DX39A_HUMAN,sp|Q13838|DX39B_HUMAN,sp|P00558|PGK1_HUMAN,sp|Q8WUA2|PPIL4_HUMAN,sp|Q02878|RL6_HUMAN,sp|P46776|RL27A_HUMAN,sp|P54105|ICLN_HUMAN,sp|Q16658|FSCN1_HUMAN,sp|P31323|KAP3_HUMAN,sp|P20290|BTF3_HUMAN,sp|Q9UJ68|MSRA_HUMAN,sp|P25705|ATPA_HUMAN,sp|Q16629|SRSF7_HUMAN,sp|O95319|CELF2_HUMAN,sp|Q13126|MTAP_HUMAN,sp|P17480|UBF1_HUMAN,sp|P42229|STA5A_HUMAN,sp|P51692|STA5B_HUMAN,sp|Q00610|CLH1_HUMAN,sp|Q16695|H31T_HUMAN,sp|P68431|H31_HUMAN,sp|P84243|H33_HUMAN,sp|Q6NXT2|H3C_HUMAN,sp|Q71DI3|H32_HUMAN,tr|Q5TEC6|Q5TEC6_HUMAN,sp|P49411|EFTU_HUMAN,sp|Q9Y2X3|NOP58_HUMAN,sp|P11940|PABP1_HUMAN,sp|Q9H1E3|NUCKS_HUMAN,sp|Q8TBC3|SHKB1_HUMAN,sp|Q13263|TIF1B_HUMAN,sp|Q53H96|P5CR3_HUMAN,sp|Q08945|SSRP1_HUMAN,sp|Q01469|FABP5_HUMAN,sp|Q99436|PSB7_HUMAN,sp|P14314|GLU2B_HUMAN,sp|Q8N8J7|F241A_HUMAN,sp|P67809|YBOX1_HUMAN,tr|A0A1W2PRB8|A0A1W2PRB8_HUMAN,sp|Q9H0W9|CK054_HUMAN,sp|P15880|RS2_HUMAN,sp|P00338|LDHA_HUMAN,sp|P54819|KAD2_HUMAN,sp|P31943|HNRH1_HUMAN,sp|P30740|ILEU_HUMAN,sp|Q9Y4E1|WAC2C_HUMAN,sp|Q641Q2|WAC2A_HUMAN,sp|P06733|ENOA_HUMAN,sp|P20042|IF2B_HUMAN,sp|P54886|P5CS_HUMAN,sp|P49915|GUAA_HUMAN,sp|Q92541|RTF1_HUMAN,sp|Q9NSD9|SYFB_HUMAN,sp|Q16666|IF16_HUMAN,sp|P23528|COF1_HUMAN,sp|Q13423|NNTM_HUMAN,sp|O94826|TOM70_HUMAN,sp|P63220|RS21_HUMAN,sp|P62805|H4_HUMAN,sp|Q9BT22|ALG1_HUMAN,sp|C9J202|AG1L2_HUMAN,sp|P55884|EIF3B_HUMAN,sp|O75663|TIPRL_HUMAN,sp|P47897|SYQ_HUMAN,sp|Q15366|PCBP2_HUMAN,sp|P50748|KNTC1_HUMAN,sp|Q7Z5L9|I2BP2_HUMAN,sp|P09429|HMGB1_HUMAN,sp|P26583|HMGB2_HUMAN,sp|O95619|YETS4_HUMAN,sp|Q14C86|GAPD1_HUMAN,sp|P53041|PPP5_HUMAN,sp|P22681|CBL_HUMAN,tr|A0A182DWH4|A0A182DWH4_HUMAN,sp|Q30154|DRB5_HUMAN,sp|P01911|2B1F_HUMAN,sp|P28066|PSA5_HUMAN,sp|Q5H9R7|PP6R3_HUMAN,sp|P18031|PTN1_HUMAN,sp|P47756|CAPZB_HUMAN,sp|P08236|BGLR_HUMAN,sp|P30626|SORCN_HUMAN,sp|O94804|STK10_HUMAN,sp|Q13620|CUL4B_HUMAN,sp|P27824|CALX_HUMAN,sp|Q86YP4|P66A_HUMAN,sp|E9PAV3|NACAM_HUMAN,sp|P51858|HDGF_HUMAN,sp|O95340|PAPS2_HUMAN,sp|O43252|PAPS1_HUMAN,sp|Q07020|RL18_HUMAN,sp|P37802|TAGL2_HUMAN,sp|Q14156|EFR3A_HUMAN,sp|O00154|BACH_HUMAN,sp|O95487|SC24B_HUMAN,sp|Q8IY67|RAVR1_HUMAN,sp|Q68EM7|RHG17_HUMAN,sp|P43243|MATR3_HUMAN,sp|P08567|PLEK_HUMAN,sp|Q9UKW4|VAV3_HUMAN,tr|A0A0C4DFX4|A0A0C4DFX4_HUMAN,sp|Q6ZRS2|SRCAP_HUMAN,sp|Q96T68|SETB2_HUMAN,sp|P08183|MDR1_HUMAN,sp|P21439|MDR3_HUMAN,sp|Q9UIA9|XPO7_HUMAN,sp|P49848|TAF6_HUMAN,sp|P00352|AL1A1_HUMAN,sp|Q86UE4|LYRIC_HUMAN,sp|P52701|MSH6_HUMAN,sp|Q5TC12|ATPF1_HUMAN,sp|P35244|RFA3_HUMAN,sp|Q96C86|DCPS_HUMAN,sp|P0DPI2|GAL3A_HUMAN,tr|A0A096LPI6|A0A096LPI6_HUMAN,sp|A0A0B4J2D5|GAL3B_HUMAN,sp|O75608|LYPA1_HUMAN,sp|P29350|PTN6_HUMAN,sp|Q16563|SYPL1_HUMAN,sp|O60508|PRP17_HUMAN,sp|P78371|TCPB_HUMAN,sp|P16150|LEUK_HUMAN,sp|P55084|ECHB_HUMAN,sp|P45880|VDAC2_HUMAN,sp|P60174|TPIS_HUMAN,sp|Q99547|MPH6_HUMAN,sp|Q15363|TMED2_HUMAN,sp|O00567|NOP56_HUMAN,sp|P55036|PSMD4_HUMAN,sp|O00541|PESC_HUMAN,sp|Q14181|DPOA2_HUMAN,sp|P35249|RFC4_HUMAN,sp|P62081|RS7_HUMAN,sp|P26196|DDX6_HUMAN,sp|P05455|LA_HUMAN,sp|P48047|ATPO_HUMAN,tr|H7C0C1|H7C0C1_HUMAN,sp|P26373|RL13_HUMAN,sp|P78527|PRKDC_HUMAN,sp|Q9Y3D7|TIM16_HUMAN,sp|Q9HC35|EMAL4_HUMAN,sp|O15305|PMM2_HUMAN,sp|Q92871|PMM1_HUMAN,sp|P29590|PML_HUMAN,sp|P62191|PRS4_HUMAN,sp|P18124|RL7_HUMAN,tr|A0A1B0GU03|A0A1B0GU03_HUMAN,sp|P07339|CATD_HUMAN,sp|Q8IVH4|MMAA_HUMAN,sp|Q15942|ZYX_HUMAN,sp|Q9H0L4|CSTFT_HUMAN,sp|P33240|CSTF2_HUMAN,sp|O75937|DNJC8_HUMAN,sp|O14672|ADA10_HUMAN,sp|O43491|E41L2_HUMAN,sp|P23246|SFPQ_HUMAN,sp|Q8ND56|LS14A_HUMAN,sp|P29401|TKT_HUMAN,sp|Q99873|ANM1_HUMAN,sp|O95433|AHSA1_HUMAN,sp|P55265|DSRAD_HUMAN,sp|P49821|NDUV1_HUMAN,sp|P49368|TCPG_HUMAN,sp|P56556|NDUA6_HUMAN,sp|Q8NF37|PCAT1_HUMAN,sp|Q99829|CPNE1_HUMAN,sp|P30041|PRDX6_HUMAN,sp|P54578|UBP14_HUMAN,sp|Q6UWD8|CP054_HUMAN,sp|P61158|ARP3_HUMAN,sp|Q00059|TFAM_HUMAN,sp|P25098|ARBK1_HUMAN,sp|Q86U90|YRDC_HUMAN,sp|P52209|6PGD_HUMAN,sp|Q6PI48|SYDM_HUMAN,sp|Q9Y617|SERC_HUMAN,sp|O94903|PLPHP_HUMAN,sp|P32519|ELF1_HUMAN,sp|Q9NVI7|ATD3A_HUMAN,sp|Q5T9A4|ATD3B_HUMAN,sp|Q6L8Q7|PDE12_HUMAN,sp|Q9H0D6|XRN2_HUMAN,sp|Q9NZL9|MAT2B_HUMAN,sp|Q2KHR2|RFX7_HUMAN,sp|O75083|WDR1_HUMAN,sp|P31146|COR1A_HUMAN,sp|P13667|PDIA4_HUMAN,sp|P13861|KAP2_HUMAN,sp|Q71UI9|H2AV_HUMAN,sp|P0C0S5|H2AZ_HUMAN,sp|P48735|IDHP_HUMAN,sp|Q9HB71|CYBP_HUMAN,sp|Q13509|TBB3_HUMAN,tr|A0A0B4J269|A0A0B4J269_HUMAN,sp|P00505|AATM_HUMAN,sp|Q9NR30|DDX21_HUMAN,sp|P27816|MAP4_HUMAN,sp|Q09472|EP300_HUMAN,sp|Q96CW1|AP2M1_HUMAN,sp|Q92769|HDAC2_HUMAN,sp|Q9BTE3|MCMBP_HUMAN,sp|P50452|SPB8_HUMAN,sp|P35237|SPB6_HUMAN,sp|P48444|COPD_HUMAN,sp|Q9NRW3|ABC3C_HUMAN,sp|Q01081|U2AF1_HUMAN,sp|Q8WU68|U2AF4_HUMAN,sp|P0DN76|U2AF5_HUMAN,tr|M0R2N4|M0R2N4_HUMAN,sp|P40939|ECHA_HUMAN,sp|Q02790|FKBP4_HUMAN,sp|O14980|XPO1_HUMAN,sp|P18433|PTPRA_HUMAN,sp|P50995|ANX11_HUMAN,sp|Q13347|EIF3I_HUMAN,sp|O15511|ARPC5_HUMAN,sp|P49721|PSB2_HUMAN,sp|Q8N7R7|CCYL1_HUMAN,sp|Q8ND76|CCNY_HUMAN,sp|P31948|STIP1_HUMAN,sp|P50991|TCPD_HUMAN,sp|Q99460|PSMD1_HUMAN,sp|Q92878|RAD50_HUMAN,sp|P62917|RL8_HUMAN,sp|P82650|RT22_HUMAN,sp|P14866|HNRPL_HUMAN,sp|P52272|HNRPM_HUMAN,sp|P37268|FDFT_HUMAN,sp|Q9BY44|EIF2A_HUMAN,sp|P04406|G3P_HUMAN,sp|Q14152|EIF3A_HUMAN,sp|Q86VP6|CAND1_HUMAN,sp|P46940|IQGA1_HUMAN,sp|Q08211|DHX9_HUMAN,sp|Q9Y3I0|RTCB_HUMAN,sp|Q9BRA2|TXD17_HUMAN,sp|O43159|RRP8_HUMAN,sp|P43686|PRS6B_HUMAN,sp|P27797|CALR_HUMAN,sp|P08559|ODPA_HUMAN,sp|Q13547|HDAC1_HUMAN,sp|Q14697|GANAB_HUMAN,sp|P09874|PARP1_HUMAN,sp|Q9NWH9|SLTM_HUMAN,sp|Q99575|POP1_HUMAN,sp|O75643|U520_HUMAN,sp|P49588|SYAC_HUMAN,sp|Q9Y6X4|F169A_HUMAN,sp|O15042|SR140_HUMAN,sp|P62937|PPIA_HUMAN,sp|Q9UKM9|RALY_HUMAN,sp|Q15365|PCBP1_HUMAN,sp|Q8IYB3|SRRM1_HUMAN,sp|Q13586|STIM1_HUMAN,sp|Q8WUK0|PTPM1_HUMAN,sp|Q6NYC8|PPR18_HUMAN,sp|P15498|VAV_HUMAN,tr|A0A2R8Y4L2|A0A2R8Y4L2_HUMAN,sp|Q8IYD1|ERF3B_HUMAN,sp|P15170|ERF3A_HUMAN,sp|Q8NBQ5|DHB11_HUMAN,sp|Q9H7N4|SFR19_HUMAN,sp|P84090|ERH_HUMAN,sp|Q9Y5K5|UCHL5_HUMAN,sp|Q9UI08|EVL_HUMAN,sp|P20292|AL5AP_HUMAN,sp|Q13094|LCP2_HUMAN,sp|P04040|CATA_HUMAN,sp|Q9BWJ5|SF3B5_HUMAN,sp|Q00839|HNRPU_HUMAN,sp|Q6ZNL6|FGD5_HUMAN,sp|O60573|IF4E2_HUMAN,sp|Q9BRB3|PIGQ_HUMAN,sp|Q96A35|RM24_HUMAN,sp|Q8WV74|NUDT8_HUMAN,sp|P35269|T2FA_HUMAN,sp|P49327|FAS_HUMAN,sp|Q14690|RRP5_HUMAN,sp|P21796|VDAC1_HUMAN,sp|P04080|CYTB_HUMAN,sp|P61604|CH10_HUMAN,sp|P08865|RSSA_HUMAN,sp|O00299|CLIC1_HUMAN,sp|P62807|H2B1C_HUMAN,sp|O60814|H2B1K_HUMAN,sp|Q99880|H2B1L_HUMAN,sp|P58876|H2B1D_HUMAN,sp|Q93079|H2B1H_HUMAN,sp|Q5QNW6|H2B2F_HUMAN,sp|Q99877|H2B1N_HUMAN,sp|P57053|H2BFS_HUMAN,sp|Q99879|H2B1M_HUMAN 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Aliphatic,8.369098712446352,15.806805708013172,16.778523489932887,15.871254162042174,16.25560538116592,6.338028169014084,15.013404825737265,14.801864801864802,14.666666666666668,14.933333333333334,14.37308868501529,17.441860465116278,11.775362318840578,5.450581395348838,12.56281407035176,16.986301369863014,15.193370165745858,17.123287671232877,4.301075268817205,5.0,14.568345323741006,12.857142857142858,9.195402298850574,17.727272727272727,11.764705882352942,5.38243626062323,12.5,12.5,16.24405705229794,13.584288052373159,18.571428571428573,15.895953757225433,17.964071856287426,15.300546448087433,9.01015228426396,12.917594654788418,13.082039911308204,13.082039911308204,13.6986301369863,11.175337186897881,11.363636363636365,12.386706948640484,9.863945578231293,9.01639344262295,12.155388471177943,16.347992351816444,14.826498422712934,15.457413249211356,10.256410256410255,11.258278145695364,14.36672967863894,13.21762349799733,13.89413988657845,15.895953757225433,15.92920353982301,16.233766233766232,14.285714285714285,15.92920353982301,12.871287128712872,11.960132890365447,12.040133779264213,17.32283464566929,3.819444444444444,14.367816091954023,9.70464135021097,16.629955947136565,13.8328530259366,14.233576642335766,14.920071047957371,10.714285714285714,17.11026615969582,15.969581749049429,7.070707070707071,15.384615384615385,13.622291021671826,14.35257410296412,14.35257410296412,18.272425249169437,16.091954022988507,12.142857142857142,5.434782608695652,12.753036437246964,11.11111111111111,13.074204946996467,13.19796954314721,13.527851458885943,14.835164835164836,12.121212121212121,12.121212121212121,14.826498422712934,14.437555358724534,12.84046692607004,11.95840554592721,12.452107279693486,12.075471698113208,11.49425287356322,14.47562776957164,13.694721825962912,16.594477531131567,12.373225152129818,10.297482837528603,16.125760649087223,11.378848728246318,10.374639769452449,14.312977099236642,11.248285322359397,13.626373626373626,17.96875,20.96069868995633,14.743589743589745,21.021897810218977,13.46153846153846,3.968253968253968,14.364640883977902,12.21498371335505,15.220700152207002,13.91891891891892,15.313028764805416,16.25615763546798,8.24742268041237,12.359550561797754,11.235955056179774,12.645590682196339,5.363984674329501,11.418685121107266,15.331807780320364,11.26126126126126,11.403508771929824,14.754098360655737,12.601626016260163,18.356456776947706,17.80821917808219,12.516469038208168,14.318181818181818,16.393442622950822,15.837937384898712,15.16802906448683,17.58957654723127,15.789473684210527,9.375,13.636363636363637,12.71186440677966,3.6363636363636367,13.81578947368421,9.051724137931036,10.473815461346632,15.881326352530541,8.667736757624397,14.754098360655739,15.654205607476634,13.66906474820144,11.991869918699187,13.888888888888888,10.81081081081081,10.970464135021096,10.344827586206897,12.679425837320574,11.650485436893204,8.085106382978724,16.636528028933093,5.042016806722689,13.779527559055119,15.194346289752652,10.471204188481675,15.994962216624684,15.501905972045742,16.83582089552239,13.970588235294118,13.970588235294118,14.705882352941178,14.814814814814815,13.970588235294118,13.970588235294118,17.035398230088497,15.689981096408317,9.748427672955975,1.646090534979424,13.861386138613861,10.658682634730539,15.328467153284672,10.860366713681241,11.851851851851851,13.71841155234657,10.227272727272727,14.393939393939394,2.1604938271604937,16.2291169451074,13.015873015873016,12.286689419795222,18.373493975903614,16.736401673640167,8.240534521158128,15.831134564643799,10.378787878787879,10.439970171513796,14.516129032258064,11.711711711711711,17.48427672955975,16.450216450216452,9.859154929577464,18.505942275042443,12.356687898089174,13.855421686746988,17.403314917127073,13.651315789473685,12.048192771084338,13.592233009708737,18.31896551724138,15.813953488372093,11.302211302211303,15.441176470588236,14.193548387096774,16.71232876712329,21.27659574468085,9.028960817717206,3.7209302325581395,3.349282296650718,13.656387665198238,15.087956698240866,13.426853707414832,12.913907284768213,12.030075187969924,11.654135338345865,11.654135338345865,15.352697095435683,15.807560137457045,13.10344827586207,16.967509025270758,13.978494623655916,10.101010101010102,13.842975206611571,16.648411829134723,11.655405405405405,12.322274881516588,9.04716073147257,6.25,14.169381107491857,12.82051282051282,12.76595744680851,13.5678391959799,17.90499390986602,11.578947368421055,13.170347003154575,16.33663366336634,11.464245175936437,12.632821723730814,14.0,15.820543093270366,13.003603013429412,13.034055727554179,11.821974965229487,17.421875,17.34059097978227,19.87120515179393,14.623338257016249,14.37125748502994,10.137457044673539,13.602941176470587,13.109756097560975,17.355371900826448,18.694362017804156,12.313432835820896,15.770609318996415,12.313432835820896,17.391304347826086,13.109243697478991,16.988416988416986,11.053540587219345,18.13084112149533,10.5,13.713080168776372,12.244897959183675,12.237762237762237,15.0,13.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