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gb1 |
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/
% gb1 refseqn:NC_000913 Calculate strand bias of bacterial genome using B1 index Program compseq output file [nc_000913.gb1]: |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gb1 reads one or more nucleotide sequences.
The output from gb1 is to a plain text file.
File: nc_000913.gb1
Sequence: NC_000913 B1: 0.0630702874711314 |
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
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) |
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