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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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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.