Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/ggcwin.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/ggcwin.txt Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,224 @@ + ggcwin +Function + + Calculates the GC content along the given genome + +Description + + ggcwin calculates and plots the GC content of the given sequence. + + 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 ggcwin + +% ggcwin refseqn:NC_000913 +Calculates the GC content along the given genome +Program compseq output file (optional) [nc_000913.ggcwin]: + + Go to the input files for this example + Go to the output files for this example + + Example 2 + +% ggcwin refseqn:NC_000913 -plot -graph png +Calculates the GC content along the given genome +Created ggcwin.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 [*.ggcwin] Program compseq output file + (optional) + + Additional (Optional) qualifiers: (none) + Advanced (Unprompted) qualifiers: + -window integer [10000] Window size to observe (Any integer + value) + -at boolean [N] Include for observing AT skew instead of + GC skew + -purine boolean [N] Include for observing purine (AG/TC) + skew + -keto boolean [N] Include for observing keto (TG/AC) skew + default: "0 + -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 + + ggcwin reads one or more nucleotide sequences. + +Output file format + + The output from ggcwin is to a plain text file or the EMBOSS graphics device. + + File: nc_000913.ggcwin + +Sequence: NC_000913 +location,GC content +0,0.520700 +10000,0.499400 +20000,0.526200 +30000,0.532300 +40000,0.527700 +50000,0.515600 +60000,0.555800 +70000,0.536000 + + [Part of this file has been deleted for brevity] + +4530000,0.442800 +4540000,0.487000 +4550000,0.507700 +4560000,0.509600 +4570000,0.444600 +4580000,0.531600 +4590000,0.512300 +4600000,0.504500 +4610000,0.535600 +4620000,0.546600 + + +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 + + ggcskew Calculates the GC skew of the input sequence + ggeneskew Calculate the gene strand bias of the given genome + ggenomicskew Calculates the GC skew in different regions of the given genom + +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. +