|   | gdeltaenc | 
   gdeltaenc calculates the codon usage bias related to translation
   optimization (delta ENC) described in Rocha (2004). The basic idea is to
   calculate the Effective Number of Codons (ENC) for highly-expressed genes
   (ribosomal genes) and weakly-expressed genes (all genes), and taking the
   relative difference between them. ENC assigns a gene a number between 20 to
   61 where 20 indicates that one codon is used for each aminoacid and 61
   indicates that each codon is used equally throughout the protein sequence.
   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/
| % gdeltaenc refseqn:NC_000913 Calculate the codon usage bias related to translation optimization (delta ENC) Program compseq output file [nc_000913.gdeltaenc]: | 
| 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 | Program compseq output file | Output file | <*>.gdeltaenc | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -[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
   gdeltaenc reads one or more nucleotide sequences.
   The output from gdeltaenc is to a plain text file.
   File: nc_000913.gdeltaenc
| Sequence: NC_000913 DELTA-ENC 0.255663430420712 | 
None.
None.
Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization, Genome Research, 14(11):2279-2286 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) | 
| gicdi | Calculates the intrinsic codon deviation index (ICDI) | 
| gsvalue | 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