|   | gcai | 
   gcai calculates codon adaptation index (CAI) for each gene. CAI is measure
   a of the relative adaptiveness of the codon usage of a gene towards the
   codon usage of highly expressed genes, ranging from 0 (no bias) to 1
   (maximum bias). CAI can be used as a 'universal' measure of codon usage
   bias as it is correlated with various gene features such as gene expression
   level, GC content, and GC skew.
   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/
| % gcai refseqn:NC_000913 Calculate codon adaptation index for each gene Codon usage output file [nc_000913.gcai]: | 
| 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 | <*>.gcai | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -translate | boolean | Include when translating using standard codon table | Boolean value Yes/No | No | 
| -wabsent | string | W value of codons absent from a reference set to negative when excludes such codons from the calculation | Any string | -1 | 
| -[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
   gcai reads one or more nucleotide sequences.
   The output from gcai is to a plain text file.
   File: nc_000913.gcai
| Sequence: NC_000913 cai,gene 0.7256,thrL 0.4831,thrA 0.4719,thrB 0.5178,thrC 0.4989,yaaX 0.4933,yaaA 0.4533,yaaJ 0.7074,talB [Part of this file has been deleted for brevity] 0.4681,yjjX 0.4797,ytjC 0.5350,rob 0.4932,creA 0.3918,creB 0.4170,creC 0.4167,creD 0.6466,arcA 0.4236,yjjY 0.3913,yjtD | 
None.
None.
Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15(3):1281-95. 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 | 
|---|---|
| gp2 | Calculate the P2 index of each gene | 
| gphx | Identify predicted highly expressed 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