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gconsensusz |
gconsensusz calculates the consensus of given list of sequences, using
Z-score. The Z-score will show higher values when the sequences are biased
to a single character within the list.
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/
% gconsensusz consensus.fasta Calculate consensus in given array of sequences Program compseq output file (optional) [rs_000000.gconsensusz]: |
% gconsensusz consensus.fasta -plot -graph png Calculate consensus in given array of sequences Created gconsensusz.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 | <*>.gconsensusz |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-high | integer | Z value greater than which is significant | Any integer value | 1 |
-low | float | Z value less than which is insignificant | Any numeric value | 0.2 |
-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
gconsensusz reads one or more nucleotide sequences.
The output from gconsensusz is to a plain text file or the EMBOSS graphics device.
File: rs_000000.gconsensusz
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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 |
---|---|
gdistincc | Calculates the distance between two loci in circular chromosomes |
gpalindrome | Searches palindrome sequences |
gseqinfo | Prints out basic nucleotide sequence statistics |
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