gfop

 

Function

Calculate the frequency of optimal codons (Fop)

Description

gfop calculates the frequency of optimal codons (Fop).Fop is an index to
show the optimization level of synonymous codon usage choice. It is
basically a ratio of optimal codons against all codons used. The value
of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
codons are used).

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 gfop

% gfop refseqn:NC_000913
Calculate the frequency of optimal codons (Fop)
Codon usage output file [nc_000913.gfop]: 

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 <*>.gfop
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-translate boolean Include when translates using standard codon table 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

gfop reads one or more nucleotide sequences.

Output file format

The output from gfop is to a plain text file.

File: nc_000913.gfop

Sequence: NC_000913
Laa,Lc,fop,gene
20,5,0.4000,thrL
819,133,0.4361,thrA
309,46,0.4783,thrB
427,69,0.5217,thrC
97,7,0.2857,yaaX
257,56,0.4643,yaaA
475,96,0.3958,yaaJ
316,56,0.6964,talB

[Part of this file has been deleted for brevity]

169,27,0.2593,yjjX
214,23,0.5652,ytjC
288,49,0.4082,rob
156,23,0.3478,creA
228,26,0.3462,creB
473,69,0.3478,creC
449,70,0.3286,creD
237,46,0.6957,arcA
45,10,0.7000,yjjY
227,24,0.2500,yjtD

Data files

None.

Notes

None.

References

   Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
      transfer RNAs and the occurrence of the respective codons in its protein
      genes: a proposal for a synonymous codon choice that is optimal for the
      E. coli translational system, J.Mol.Biol, 151:389-409.

   Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
      organisms, Mol.Biol.Evol, 2(1):13-34.

   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)
gscs Calculates the scaled chi-square
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.