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gbaseentropy |
This function calculates and graphs the sequence conservation in regions
around the start/stop codons using Shanon uncertainty (entropy). Smaller
values resemble higher conservation where the minumum value is 0 and the
maximum value is 2. The entropy is typically the lowest around position 0
(start/stop codon position).
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/
% gbaseentropy refseqn:NC_000913 Calculates and graphs the sequence conservation using Shanon uncertainty (entropy) Program compseq output file (optional) [nc_000913.gbaseentropy]: |
% gbaseentropy refseqn:NC_000913 -plot -graph png Calculates and graphs the sequence conservation using Shanon uncertainty (entropy) Created gbaseentropy.1.png |
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 |
-graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg | EMBOSS_GRAPHICS value, or x11 |
-outfile | outfile | Program compseq output file (optional) | Output file | <*>.gbaseentropy |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-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 |
-plot | toggle | Include to plot result | Toggle value Yes/No | No |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gbaseentropy reads one or more nucleotide sequences.
The output from gbaseentropy is to a plain text file or the EMBOSS graphics device.
File: nc_000913.gbaseentropy
Sequence: NC_000913 -30,1.98284 -29,1.97873 -28,1.97692 -27,1.97595 -26,1.97094 -25,1.96777 -24,1.96272 -23,1.96288 -22,1.95707 [Part of this file has been deleted for brevity] 21,1.93528 22,1.94470 23,1.95204 25,1.93139 25,1.95640 26,1.95711 27,1.93785 28,1.96060 29,1.94316 30,1.92581 |
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 |
---|---|
gbaseinformationcontent | Calculates and graphs the sequence conservation using information content |
gbaserelativeentropy | Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy) |
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