![]() |
gb2 |
gb2 calculates strand bias of bacterial genome using B2 index,
proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate
the distance from neutral parity state (0.5, 0.5), when the bias of
the coding regions is 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 transcription- and translation-associated effects of
bias from Chargaff's second parity rule.
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/
% gb2 refseqn:NC_000913 Calculate strand bias of bacterial genome using B2 index Program compseq output file [nc_000913.gb2]: |
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 | <*>.gb2 |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gb2 reads one or more nucleotide sequences.
The output from gb2 is to a plain text file.
File: nc_000913.gb2
Sequence: NC_000913 B2: 0.0919769585775651 |
None.
None.
Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in bacteria, Genome Biology, 3(10):0058 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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
gb1 | Calculate strand bias of bacterial genome using B1 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) |
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