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gsignature |
gsignature calculates short oligonuleotide usage (genomic signture),
defined as the ratio of observed (O) to expected (E) oligonucleotide
frequencies. It is known that the genomic signature stays constant
throughout the genome.
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/
% gsignature refseqn:NC_000913 Calculate oligonucleotide usage (genomic signature) Program compseq output file [nc_000913.gsignature]: |
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 | <*>.gsignature |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-wordlength | integer | Word length | Any integer value | 2 |
-[no]bothstrand | boolean | Include to use both strands direct used otherwise | Boolean value Yes/No | Yes |
-[no]oe | boolean | Include to use O/E value observed values used otherwise | Boolean value Yes/No | Yes |
-[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
gsignature reads one or more nucleotide sequences.
The output from gsignature is to a plain text file.
File: nc_000913.gsignature
Sequence: NC_000913 aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,memo 1.206,0.884,0.817,1.103,1.117,0.905,1.159,0.817,0.922,1.283,0.905,0.884,0.755,0.922,1.117,1.206, |
None.
None.
Campbell A et al. (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA, Proc Natl Acad Sci U S A. 96(16):9184-9. Karlin S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes, Trends Microbiol. 9(7):335-43. 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 |
---|---|
gkmertable | Create an image showing all k-mer abundance within a sequence |
gnucleotideperiodicity | Checks the periodicity of certain oligonucleotides |
goligomercounter | Counts the number of given oligomers in a sequence |
goligomersearch | Searches oligomers in given sequence |
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