gscs

 

Function

Calculates the scaled chi-square

Description

gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS
are calculated using completely synonymous codon usage as the expectation
and then scaled by dividing the value by the number of codons in the gene
excluding Trp and Met.

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 gscs

% gscs refseqn:NC_000913
Calculates the scaled chi-square
Codon usage output file [nc_000913.gscs]: 

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 <*>.gscs
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

Input file format

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

gscs reads one or more nucleotide sequences.

Output file format

The output from gscs is to a plain text file.

File: nc_000913.gscs

Sequence: NC_000913
scs,gene
1.4458,thrL
0.3122,thrA
0.2551,thrB
0.4104,thrC
0.3084,yaaX
0.3230,yaaA
0.2957,yaaJ
0.7101,talB

[Part of this file has been deleted for brevity]

0.3054,yjjX
0.4076,ytjC
0.4231,rob
0.3903,creA
0.3472,creB
0.2695,creC
0.3500,creD
0.5077,arcA
0.4576,yjjY
0.2926,yjtD

Data files

None.

Notes

None.

References

   Comeron JM., Aguade M. (1998) An evaluation of measures of synonymous
      codon usage bias, J Mol Evol, 47(3):268-74.

   Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis
      reflects both translational selection and mutational biases,
      15(19):8023-40.

   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
genc Calculate the effective number of codons (Nc)
gew Calculate a measure of synonymous codon usage evenness (Ew)
gfop Calculate the frequency of optimal codons (Fop)
gwvalue Calculate the 'relative adaptiveness of each codon' (W)

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.