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gsvalue |
gsvalue calculates the strength of selected codon usage bias (S), also
known as Sharp's S index. Using four codon pairs that are recognized by the
same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and
UAU), and Asn(AAC and AAU), since the former in each of the pairs has
stronger Watson-Crick pairing, selection towards the former codon can be
observed for highly expressed genes. S index is therefore the weighted
average of such bias, giving an over-all value for a genome, indicating its
strength of selected codon usage bias. See Sharp et al. (2005) for details.
Sharp originally defined 40 genes as the highly expressed gene group, with
tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton
of these genes is not convenient for computational automation, by default,
this method uses ribosomal proteins as the highly expressed gene group,
as used by Viera-silva and Rocha (2010).
However, Sharp's gene group can be optionally used with -sharp option.
With this option, all of the 40 genes must be named accordingly in the given
genome file.
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/
Here is a sample session with gsvalue % gsvalue refseqn:NC_000913 Calculate the strength of selected codon usage bias (S) Codon usage output file [nc_000913.gsvalue]: |
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 | <*>.gsvalue |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-sharp | boolean | Include to use the 40 genes used by Sharp instead of ribosomal proteins | Boolean value Yes/No | No |
-[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
gsvalue reads one or more nucleotide sequences.
The output from gsvalue is to a plain text file.
File: nc_000913.gsvalue
Sequence: NC_000913 S-value: 1.23467100598485 |
None.
None.
Sharp PM et al. (2005) "Variation in the strength of selected codon usage bias among bacteria", Nucleic Acids Research, 33(4):1141-1153 Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808 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) |
gdeltaenc | Calculate the codon usage bias related to translation optimization (delta ENC) |
gicdi | Calculates the intrinsic codon deviation index (ICDI) |
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