|   | gicdi | 
   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/
| % gicdi refseqn:NC_000913 Calculates the intrinsic codon deviation index (ICDI) Codon usage output file [nc_000913.gicdi]: | 
| 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 | <*>.gicdi | 
| 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
   gicdi reads one or more nucleotide sequences.
   The output from gicdi is to a plain text file.
   File: nc_000913.gicdi
| Sequence: NC_000913 icdi,gene 0.8192,thrL 0.1258,thrA 0.1127,thrB 0.1689,thrC 0.3099,yaaX 0.2030,yaaA 0.1600,yaaJ 0.3533,talB [Part of this file has been deleted for brevity] 0.2203,yjjX 0.2719,ytjC 0.1377,rob 0.2647,creA 0.1944,creB 0.1733,creC 0.1926,creD 0.2728,arcA 0.5171,yjjY 0.2434,yjtD | 
None.
None.
Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes, Gene, 139:43-49. 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 | 
|---|---|
| gcbi | Calculates the codon bias index (CBI) | 
| gdelta_enc | Calculate the codon usage bias related to translation optimization (delta ENC) | 
| gs_value | Calculate the strength of selected codon usage bias (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