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gbasezvalue |
This function calculates and extracts conserved oligomers per position using
Z-score, in regions around the start/stop codons. The oligomers are returned
in ranking order up to "-limit" number.
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/
% gbasezvalue refseqn:NC_000913 Extracts conserved oligomers per position using Z-score Program compseq output file (optional) [nc_000913.gbasezvalue]: |
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 (optional) | Output file | <*>.gbasezvalue |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-limit | integer | Rank threshold for showing the conserved oligomer | Any integer value | 5 |
-position | selection | Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM | Choose from selection list of values | start |
-patlen | integer | Length of oligomer to count | Any integer value | 3 |
-upstream | integer | Length upstream of specified position to create PWM | Any integer value | 30 |
-downstream | integer | Length downstream of specified position to create PWM | Any integer value | 30 |
-[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
gbasezvalue reads one or more nucleotide sequences.
The output from gbasezvalue is to a plain text file.
File: nc_000913.gbasezvalue
Sequence: NC_000913 position:-30,1,taa,-0.76525 2,aga,-0.79101 3,tta,-1.14174 4,cta,-1.18831 5,aat,-1.86652 position:-29,1,cta,-0.18368 2,aat,-0.71851 3,gac,-1.26182 4,taa,-1.39455 [Part of this file has been deleted for brevity] position:29,1,gct,1.66288 2,act,1.26637 3,tat,0.66721 4,cct,-0.43158 5,tgt,-0.59254 position:30,1,ctg,3.12072 2,att,0.04193 3,ctc,-0.12416 4,cta,-0.38461 5,tta,-0.76413 |
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 |
---|---|
gbase_counter | Creates a position weight matrix of oligomers around start codon |
gview_cds | Displays a graph of nucleotide contents around start and stop codons |
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