Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gbaseinformationcontent.txt @ 0:8300eb051bea draft
Initial upload
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/gbaseinformationcontent.txt Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,239 @@ + gbaseinformationcontent +Function + + Calculates and graphs the sequence conservation using information content + +Description + + This function calculates and graphs the sequence conservation in regions + around the start/stop codons using information content. Values are obtained + by subtracting the entropy for each positfion from the maximum possible + value (which will be 2 in the case of nucleotide sequences). Information + content will show the highest value when the frequency is most biased to a + single alphabet. + + Information content I is obtained by subtracting the entropy H from the + maximum uncertainty log(2,|M|): + I(P(i)) = log(2,|M|) - (-sum(P(i,j) * log(2,P(i,j)))) + + 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 gbaseinformationcontent + +% gbaseinformationcontent refseqn:NC_000913 +Calculates and graphs the sequence conservation using information content +Program compseq output file (optional) [nc_000913.gbaseinformationcontent]: + + Go to the input files for this example + Go to the output files for this example + + Example 2 + +% gbaseinformationcontent refseqn:NC_000913 -plot -graph png +Calculates and graphs the sequence conservation using information content +Created gbaseinformationcontent.1.png + + Go to the input files for this example + Go to the output files for this example + +Command line arguments + + Standard (Mandatory) qualifiers (* if not always prompted): + [-sequence] seqall Nucleotide sequence(s) filename and optional + format, or reference (input USA) +* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type + (ps, hpgl, hp7470, hp7580, meta, cps, x11, + tek, tekt, none, data, xterm, png, gif, svg) +* -outfile outfile [*.gbaseinformationcontent] Program compseq + output file (optional) + + Additional (Optional) qualifiers: (none) + Advanced (Unprompted) qualifiers: + -position selection [start] Either 'start' (around start codon) + or 'end' (around stop codon) to create the + PWM + -upstream integer [30] Length upstream of specified position + to create PWM (Any integer value) + -downstream integer [30] Length downstream of specified position + to create PWM (Any integer value) + -patlen integer [3] Length of oligomer to count (Any integer + value) + -[no]accid boolean [Y] Include to use sequence accession ID as + query + -plot toggle [N] Include to plot result + + 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 + + "-graph" associated qualifiers + -gprompt boolean Graph prompting + -gdesc string Graph description + -gtitle string Graph title + -gsubtitle string Graph subtitle + -gxtitle string Graph x axis title + -gytitle string Graph y axis title + -goutfile string Output file for non interactive displays + -gdirectory string Output directory + + "-outfile" associated qualifiers + -odirectory 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 + + gbaseinformationcontent reads one or more nucleotide sequences. + +Output file format + + The output from gbaseinformationcontent is to a plain text file or the + EMBOSS graphics device. + + File: nc_000913.gbaseinformationcontent + +Sequence: NC_000913 +-30,2.42457 +-29,2.42811 +-28,2.43235 +-27,2.43116 +-26,2.44278 +-25,2.44236 +-24,2.44502 +-23,2.46097 +-22,2.46588 + + [Part of this file has been deleted for brevity] + +21,2.27547 +22,2.46974 +23,2.46342 +24,2.32686 +25,2.46245 +26,2.46061 +27,2.27664 +28,2.45650 +29,2.48206 +30,2.29140 + + +Data files + + None. + +Notes + + None. + +References + + 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 + + gbaseentropy Calculates and graphs the sequence conservation + using Shanon uncertainty (entropy) + gbaserelativeentropy Calculates and graphs the sequence conservation + using Kullback-Leibler divergence (relative + entropy) + +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. +