gdeltagcskew

 

Function

Calculate strand bias of bacterial genome using delta GC skew index

Description

gdeltagcskew calculates strand bias of bacterial genome using delta GC skew
index, first proposed by Rocha et al. (2001), and further extended in 2006.
Basic idea of delta GC skew index is to calculate the difference of GC skew
in coding regions residing in leading and lagging strands. Rocha et al.
(2001) calculates delta GC skew index using the third codon position of
genes, and Rocha et al. (2006) modified to only use >fourfold degenerate
codons.

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 gdeltagcskew

% gdeltagcskew refseqn:NC_000913
Calculate strand bias of bacterial genome using delta GC skew index
Program compseq output file [nc_000913.gdeltagcskew]: 

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 Program compseq output file Output file <*>.gdeltagcskew
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-at boolean Include when observing AT skew instead of GC skew Boolean value Yes/No No
-purine boolean Include when observing purine (AG/TC) skew Boolean value Yes/No No
-keto boolean Include when observing keto (TG/AC) skew Boolean value Yes/No No
-method selection Choose the nucleotides to use 'degenerate', 'gc3', or 'all' Choose from selection list of values degenerate
-[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

gdeltagcskew reads one or more nucleotide sequences.

Output file format

The output from gdeltagcskew is to a plain text file.

File: nc_000913.gdeltagcskew

Sequence: NC_000913 DELTA-GCskew -0.108937

Data files

None.

Notes

None.

References

   Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
      Genomes, Molecular Biology and Evolution, 18(9):1789-1799

   Rocha EPC et al. (2006) Similar compositional biases are caused by very
      different mutational effects, Genome Research, 16:1537-1547

   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
gb1 Calculate strand bias of bacterial genome using B1 index
gb2 Calculate strand bias of bacterial genome using B2 index
ggcsi GC Skew Index: an index for strand-specefic mutational bias
glda_bias Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)

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.