Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gphx.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/gphx.txt Fri Jun 26 05:20:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,211 +0,0 @@ - gphx -Function - - Identify predicted highly expressed gene - -Description - - gphx calculates codon usage differences between gene classes for identifying - Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is - identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's - nature. PHX genes are known to generally have favorable codon usage, strong - SD sequences, and probably stronger conservation of promoter sequences. - A gene is idenfitied as PA if BgC and BgH is greater than the median of - BgC for every gene with a length close to the gene. - - 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 gphx - -% gphx refseqn:NC_000913 -Identify predicted highly expressed gene -Codon usage output file [nc_000913.gphx]: - - 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 [*.gphx] Codon usage output file - - Additional (Optional) qualifiers: (none) - Advanced (Unprompted) qualifiers: - -translate boolean [N] Include when translating using standard - codon table - -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular - expression to delete key (Any string) - -[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 - - gphx reads one or more nucleotide sequences. - -Output file format - - The output from gphx is to a plain text file. - - File: nc_000913.gphx - -Sequence: NC_000913 -BgC,BgH,E_g,phx,pa,gene -0.8070,0.8977,0.8990,0,1,thrL -0.1857,0.5958,0.3116,0,0,thrA -0.2323,0.5964,0.3896,0,0,thrB -0.2353,0.6064,0.3881,0,0,thrC -0.4353,0.6020,0.7231,0,1,yaaX -0.2961,0.6790,0.4361,0,0,yaaA -0.2233,0.7009,0.3186,0,0,yaaJ -0.4149,0.3071,1.3511,1,0,talB - - [Part of this file has been deleted for brevity] - -0.3255,0.7038,0.4625,0,0,yjjX -0.3531,0.5906,0.5979,0,0,ytjC -0.2257,0.5235,0.4311,0,0,rob -0.3584,0.6809,0.5264,0,0,creA -0.3455,0.7950,0.4346,0,0,creB -0.2298,0.7154,0.3212,0,0,creC -0.3299,0.7916,0.4167,0,0,creD -0.3543,0.3786,0.9357,0,0,arcA -0.7295,0.8286,0.8804,0,1,yjjY -0.4028,0.8401,0.4795,0,0,yjtD - - -Data files - - None. - -Notes - - None. - -References - - CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm - - Henry I., Sharp PM. (2007) Predicting gene expression level from codon - usage bias Mol Biol Evol, 24(1):10-2. - - Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse - prokaryotic genomes J.Bacteriol, 182(18):5238-5250. - - 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 - - gcai Calculate codon adaptation index for each gene - gp2 Calculate the P2 index of each gene - -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. -