gsvalue

 

Function

Calculate the strength of selected codon usage bias (S)

Description

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/

Usage


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]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

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

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gsvalue reads one or more nucleotide sequences.

Output file format

The output from gsvalue is to a plain text file.

File: nc_000913.gsvalue

Sequence: NC_000913 S-value: 1.23467100598485

Data files

None.

Notes

None.

References

   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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

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)

Author(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

History

2012 - Written by Hidetoshi Itaya

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scrips.

Comments

None.