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gldabias |
gldabias calculates strand bias of bacterial genome using linear
discriminant analysis (LDA), as proposed in Reference 1. The basic idea is
to use composition data of genes to train and predict the strand of genes
residing either on the leading or the lagging strand. For computational
efficiency, this method trans and predicts the strands at putative
replication origin as reported by the rep_ori_ter() method. This usually
results in maximum predictability of LDA within bacterial genomes.
Data to use for LDA can be chosen from "base", "codonbase", "codon", and
"amino", with -variable option.
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/
% gldabias refseqn:NC_000913 Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) Program compseq output file [nc_000913.gldabias]: |
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 | <*>.gldabias |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-coefficients | integer | Show LDA coefficients | Any integer value | 0 |
-variable | selection | Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino' | Choose from selection list of values | codon |
-[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
gldabias reads one or more nucleotide sequences.
The output from gldabias is to a plain text file.
File: nc_000913.gldabias
Sequence: NC_000913 LDA-BIAS: 0.742533 |
None.
None.
Rocha EPC et al. (1999) "Universal replication biases in bacteria", Molecular Microbiology, 32(1):11-16 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 |
gdeltagcskew | Calculate strand bias of bacterial genome using delta GC skew |
ggcsi | GC Skew Index: an index for strand-specefic mutational bias |
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