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genc |
genc calculates the effective number of codons (ENC|Nc). ENC is a measure
for species-independent codon usage bias. Some measures including CAI are
species-dependent as optimal codons differ. ENC assigns a gene a number
between 20 to 61 where 20 indicates that one codon is used for each amino
acid 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/
% genc refseqn:NC_000913 Calculate the effective number of codons (Nc) Codon usage output file [nc_000913.genc]: |
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 | <*>.genc |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-translate | boolean | Include when translates using standard codon table | Boolean value Yes/No | No |
-delkey | string | Regular expression to delete key (i.e. amino acids and nucleotides) | 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
genc reads one or more nucleotide sequences.
The output from genc is to a plain text file.
File: nc_000913.genc
Sequence: NC_000913 enc,gene ,thrL 48.41,thrA 54.13,thrB 46.18,thrC 51.65,yaaX 45.71,yaaA 48.54,yaaJ 36.83,talB [Part of this file has been deleted for brevity] 51.43,yjjX 46.61,ytjC 49.83,rob 47.74,creA 50.63,creB 51.39,creC 48.42,creD 41.53,arcA 61,yjjY 53.63,yjtD |
None.
None.
Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Wright F. (1990) The 'effective number of codons' used in a gene, Gene, 87:23-29. 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 |
---|---|
gew | Calculate a measure of synonymous codon usage evenness (Ew) |
gfop | Calculate the frequency of optimal codons (Fop) |
gscs | Calculates the scaled chi-square |
gwvalue | Calculate the 'relative adaptiveness of each codon' (W) |
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