Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/ggenomicskew.txt @ 2:8947fca5f715 draft default tip
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| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:21:44 -0400 |
| parents | 84a17b3fad1f |
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--- a/GEMBASSY-1.0.3/doc/text/ggenomicskew.txt Fri Jun 26 05:20:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,225 +0,0 @@ - ggenomicskew -Function - - Calculates the GC skew in different regions of the given genome - -Description - - ggenomicskew calculates and plots the GC skew for the whole genome, coding - regions, intergenic regions, and the third codon. This program is useful in - visualizing various base composition bias within the genome. AT skew can be - calculated instead of GC skew by toggling the -at qualifier. - - 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 ggenomicskew - -% ggenomicskew refseqn:NC_000913 -Calculates the GC skew in different regions of the given genome -Program compseq output file (optional) [nc_000913.ggenomicskew]: - - Go to the input files for this example - Go to the output files for this example - - Example 2 - -% ggenomicskew refseqn:NC_000913 -plot -graph png -Calculates the GC skew in different regions of the given genome -Created ggenomicskew.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 [*.ggenomicskew] Program compseq output file - (optional) - - Additional (Optional) qualifiers: (none) - Advanced (Unprompted) qualifiers: - -divide integer [250] Window to divide into (Any integer - value) - -at boolean [N] Input 1 when observing AT skew instead - of GC skew - -[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 - - ggenomicskew reads one or more nucleotide sequences. - -Output file format - - The output from ggenomicskew is to a plain text file or the EMBOSS graphics device. - - File: nc_000913.ggenomicskew - -Sequence: NC_000913 -location,GC skew,coding,intergenic,third codon -0,-0.036259,-0.040085,-0.034707,-0.141888, -1,-0.031167,-0.035657,0.047953,-0.175758, -2,-0.028670,-0.031139,-0.049143,-0.018466, -3,-0.016647,-0.004656,-0.102616,0.086181, -4,-0.041985,-0.029846,-0.088670,0.015291, -5,-0.097093,-0.103813,-0.067275,-0.247401, -6,-0.028028,-0.016363,-0.048806,-0.047332, -7,-0.055805,-0.059329,-0.020071,-0.123271, - - [Part of this file has been deleted for brevity] - -241,0.000772,-0.012151,-0.063786,0.069585, -242,-0.025787,-0.000384,-0.049143,0.029431, -243,0.010516,0.008217,-0.030600,0.128657, -244,-0.037115,-0.015134,0.017500,0.035398, -245,-0.000317,0.006021,-0.047170,0.091549, -246,-0.025417,-0.015190,-0.116608,0.044619, -247,-0.038404,-0.035676,-0.135714,0.015375, -248,-0.026246,-0.024240,-0.037190,-0.130118, -249,-0.053371,-0.057225,-0.022472,-0.082167, -250,-0.026316,0.166667,-0.151515,0.000000, - - -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 - ggeneskew Calculate the gene strand bias of the given genome - -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. -