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goligomersearch |
goligomersearch searches for the given oligomer in given sequence. Oligomer
can be specified using degenerate nucleotide alphabet, or by regular
expressions. Performance is optimized for fast searching.
This method changes the returning value according to the given options.
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/
% goligomersearch refseqn:NC_000913 atgcatgc Searches oligomers in given sequence Program compseq output file [nc_000913.goligomersearch]: |
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 search | Any string | |
[-outfile] (Parameter 3) |
outfile | Program compseq output file | Output file | <*>.goligomersearch |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-return | selection | 'position' to return list of positions where oligomers are found, 'oligo' to return list of oligomers found ordered by positions, 'both' to return a hash with positions as keys and oligomers as values, 'distribution' to return four values about the distribution of given oligomer | Choose from selection list of values | position |
-[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
goligomersearch reads one or more nucleotide sequences.
The output from goligomersearch is to a plain text file.
File: nc_000913.goligomersearch
Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391 |
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 |
goligomercounter | Counts the number of given oligomers in a 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