gb1

 

Function

Calculate strand bias of bacterial genome using B1 index

Description

gb1 calculates the strand bias of bacterial genome using B1 index,
first proposed by Lobry and Sueoka (2002), and further extended by
Rocha et al. (2006). Basic idea of B1 index is to calculate the
distance between the two strands, when the leading and lagging strands
are plotted in a coordinate system with axes representing G/(G+C) and
A/(A+T), using the third codon position of genes. This index measures the
degree of replication-induced bias from Chargaff's second parity rule.
Rocha et al. modified B1 index to only use >fourfold degenerate codons,
and to use T/(A+T) in place of A/(A+T).

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 gb1

% gb1 refseqn:NC_000913
Calculate strand bias of bacterial genome using B1 index
Program compseq output file [nc_000913.gb1]: 

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 <*>.gb1
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-method selection Choose method of 'lobry' or 'rocha' Choose from selection list of values rocha
-[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

gb1 reads one or more nucleotide sequences.

Output file format

The output from gb1 is to a plain text file.

File: nc_000913.gb1

Sequence: NC_000913 B1: 0.0630702874711314

Data files

None.

Notes

None.

References

   Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
      bacteria, Genome Biology, 3(10):0058

   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
gb2 Calculate strand bias of bacterial genome using B2 index
gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
ggcsi GC Skew Index: an index for strand-specefic mutational bias
gldabias 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.