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gdeltagcskew |
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/
% gdeltagcskew refseqn:NC_000913 Calculate strand bias of bacterial genome using delta GC skew index Program compseq output file [nc_000913.gdeltagcskew]: |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gdeltagcskew reads one or more nucleotide sequences.
The output from gdeltagcskew is to a plain text file.
File: nc_000913.gdeltagcskew
Sequence: NC_000913 DELTA-GCskew -0.108937 |
None.
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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.
None.
None.
It always exits with a status of 0.
None.
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) |
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