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goligomercounter |
goligomercounter counts the number of oligomers in a sequence (by windows
optionally). Oligomer can be specified using degenerate nucleotide alphabet,
or by regular expressions. k-mers can be counted by specifying the "-length"
qualifier.
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/
% goligomercounter refseqn:NC_000913 atgcatgc Counts the number of given oligomers in a sequence Program compseq output file [nc_000913.goligomercounter]: |
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 |
[-oligomer] (Parameter 2) |
string | Oligomer to count | Any string | |
[-outfile] (Parameter 3) |
outfile | Program compseq output file | Output file | <*>.goligomercounter |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-window | integer | Int window size | Any integer value | 0 |
-[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
goligomercounter reads one or more nucleotide sequences.
The output from goligomercounter is to a plain text file.
File: nc_000913.goligomercounter
Sequence: NC_000913 Oligomer: atgcatgc Number: 27 |
None.
None.
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 |
goligomersearch | Searches oligomers in given sequence |
gsignature | Calculate oligonucleotide usage (genomic signature) |
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