|   | gphx | 
   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/
| % gphx refseqn:NC_000913 Identify predicted highly expressed gene Codon usage output file [nc_000913.gphx]: | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| [-outfile] (Parameter 2) | outfile | Codon usage output file | Output file | <*>.gphx | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -translate | boolean | Include when translating using standard codon table | Boolean value Yes/No | No | 
| -delkey | string | Regular expression to delete key | Any string | [^ACDEFGHIKLMNPQRSTVWYacgtU] | 
| -[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes | 
   The database definitions for following commands are available at
   http://soap.g-language.org/kbws/embossrc
   gphx reads one or more nucleotide sequences.
   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 | 
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
| Program name | Description | 
|---|---|
| gcai | Calculate codon adaptation index for each gene | 
| gp2 | Calculate the P2 index of each gene | 
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