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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