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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
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ggeneskew Function Calculate the gene strand bias of the given genome Description ggeneskew calculates and plots the strand bias of genes (or the GC skew within them). By default, this program visualizes the gene strand preference (1 for direct, -1 for complement strand), but by specifying -base option option, GC/AT/Purine/Keto skews of the coding regions or more specifically in the GC3 (third codon position) with -gctri option can be calculated. 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 ggeneskew % ggeneskew refseqn:NC_000913 Calculate the gene strand bias of the given genome Program compseq output file (optional) [nc_000913.ggeneskew]: Go to the input files for this example Go to the output files for this example Example 2 % ggeneskew refseqn:NC_000913 -plot -graph png Calculate the gene strand bias of the given genome Created ggeneskew.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 [*.ggeneskew] Program compseq output file (optional) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -window integer [10000] Window size to observe (Any integer value) -slide integer [10000] Window slide size (Any integer value) -cumulative boolean [N] Input 1 to calculate cumulative skew -base selection [none] Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews -gctri boolean [N] Include to use only the third codon positions -[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 ggeneskew reads one or more nucleotide sequences. Output file format The output from ggeneskew is to a plain text file or the EMBOSS graphics device. File: nc_000913.ggeneskew Sequence: NC_000913 location,gene None skew 190,0.294118 337,-0.058914 2801,-0.120000 3734,-0.070588 5234,0.037500 5683,0.020725 6529,0.032765 8238,-0.028226 [Part of this file has been deleted for brevity] 4631820,-0.093407 4632464,-0.006479 4633544,-0.120690 4634030,-0.060367 4634719,-0.104167 4636201,-0.144560 4637613,0.010929 4638425,0.200000 4638965,-0.081871 , 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 ggcwin Calculates the GC content along 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.