Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gfop.txt @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/doc/text/gfop.txt Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,209 @@ + gfop +Function + + Calculate the frequency of optimal codons (Fop) + +Description + + gfop calculates the frequency of optimal codons (Fop).Fop is an index to + show the optimization level of synonymous codon usage choice. It is + basically a ratio of optimal codons against all codons used. The value + of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal + codons are used). + + G-language SOAP service is provided by the + Institute for Advanced Biosciences, Keio University. + The original web service is located at the following URL: + + http://www.g-language.org/wiki/soap + + WSDL(RPC/Encoded) file is located at: + + http://soap.g-language.org/g-language.wsdl + + Documentation on G-language Genome Analysis Environment methods are + provided at the Document Center + + http://ws.g-language.org/gdoc/ + +Usage + +Here is a sample session with gfop + +% gfop refseqn:NC_000913 +Calculate the frequency of optimal codons (Fop) +Codon usage output file [nc_000913.gfop]: + + Go to the input files for this example + Go to the output files for this example + +Command line arguments + + Standard (Mandatory) qualifiers: + [-sequence] seqall Nucleotide sequence(s) filename and optional + format, or reference (input USA) + [-outfile] outfile [*.gfop] Codon usage output file + + Additional (Optional) qualifiers: (none) + Advanced (Unprompted) qualifiers: + -translate boolean [N] Include when translates using standard + codon table + -[no]accid boolean [Y] Include to use sequence accession ID as + query + + Associated qualifiers: + + "-sequence" associated qualifiers + -sbegin1 integer Start of each sequence to be used + -send1 integer End of each sequence to be used + -sreverse1 boolean Reverse (if DNA) + -sask1 boolean Ask for begin/end/reverse + -snucleotide1 boolean Sequence is nucleotide + -sprotein1 boolean Sequence is protein + -slower1 boolean Make lower case + -supper1 boolean Make upper case + -scircular1 boolean Sequence is circular + -sformat1 string Input sequence format + -iquery1 string Input query fields or ID list + -ioffset1 integer Input start position offset + -sdbname1 string Database name + -sid1 string Entryname + -ufo1 string UFO features + -fformat1 string Features format + -fopenfile1 string Features file name + + "-outfile" associated qualifiers + -odirectory2 string Output directory + + General qualifiers: + -auto boolean Turn off prompts + -stdout boolean Write first file to standard output + -filter boolean Read first file from standard input, write + first file to standard output + -options boolean Prompt for standard and additional values + -debug boolean Write debug output to program.dbg + -verbose boolean Report some/full command line options + -help boolean Report command line options and exit. More + information on associated and general + qualifiers can be found with -help -verbose + -warning boolean Report warnings + -error boolean Report errors + -fatal boolean Report fatal errors + -die boolean Report dying program messages + -version boolean Report version number and exit + +Input file format + + The database definitions for following commands are available at + http://soap.g-language.org/kbws/embossrc + + gfop reads one or more nucleotide sequences. + +Output file format + + The output from gfop is to a plain text file. + + File: nc_000913.gfop + +Sequence: NC_000913 +Laa,Lc,fop,gene +20,5,0.4000,thrL +819,133,0.4361,thrA +309,46,0.4783,thrB +427,69,0.5217,thrC +97,7,0.2857,yaaX +257,56,0.4643,yaaA +475,96,0.3958,yaaJ +316,56,0.6964,talB + + [Part of this file has been deleted for brevity] + +169,27,0.2593,yjjX +214,23,0.5652,ytjC +288,49,0.4082,rob +156,23,0.3478,creA +228,26,0.3462,creB +473,69,0.3478,creC +449,70,0.3286,creD +237,46,0.6957,arcA +45,10,0.7000,yjjY +227,24,0.2500,yjtD + + +Data files + + None. + +Notes + + None. + +References + + Ikemura, T. (1981) Correlation between the abundance of Escherichia coli + transfer RNAs and the occurrence of the respective codons in its protein + genes: a proposal for a synonymous codon choice that is optimal for the + E. coli translational system, J.Mol.Biol, 151:389-409. + + Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular + organisms, Mol.Biol.Evol, 2(1):13-34. + + Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and + Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench + for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. + + Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for + large-scale analysis of high-throughput omics data, J. Pest Sci., + 31, 7. + + Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome + Analysis Environment with REST and SOAP Web Service Interfaces, + Nucleic Acids Res., 38, W700-W705. + +Warnings + + None. + +Diagnostic Error Messages + + None. + +Exit status + + It always exits with a status of 0. + +Known bugs + + None. + +See also + + genc Calculate the effective number of codons (Nc) + gew Calculate a measure of synonymous codon usage evenness (Ew) + gscs Calculates the scaled chi-square + gwvalue Calculate the 'relative adaptiveness of each codon' (W) + +Author(s) + + Hidetoshi Itaya (celery@g-language.org) + Institute for Advanced Biosciences, Keio University + 252-0882 Japan + + Kazuharu Arakawa (gaou@sfc.keio.ac.jp) + Institute for Advanced Biosciences, Keio University + 252-0882 Japan + +History + + 2012 - Written by Hidetoshi Itaya + 2013 - Fixed by Hidetoshi Itaya + +Target users + + This program is intended to be used by everyone and everything, from + naive users to embedded scripts. + +Comments + + None. +