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ggcwin |
ggcwin calculates and plots the GC content of the given sequence.
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/
% ggcwin refseqn:NC_000913 Calculates the GC content along the given genome Program compseq output file (optional) [nc_000913.ggcwin]: |
% ggcwin refseqn:NC_000913 -plot -graph png Calculates the GC content along the given genome Created ggcwin.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 | <*>.ggcwin |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-window | integer | Window size to observe | Any integer value | 10000 |
-at | boolean | Include for observing AT skew instead of GC skew | Boolean value Yes/No | No |
-purine | boolean | Include for observing purine (AG/TC) skew | Boolean value Yes/No | No |
-keto | boolean | Include for observing keto (TG/AC) skew default: "0 | Boolean value Yes/No | No |
-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
ggcwin reads one or more nucleotide sequences.
The output from ggcwin is to a plain text file or the EMBOSS graphics device.
File: nc_000913.ggcwin
Sequence: NC_000913 location,GC content 0,0.520700 10000,0.499400 20000,0.526200 30000,0.532300 40000,0.527700 50000,0.515600 60000,0.555800 70000,0.536000 [Part of this file has been deleted for brevity] 4530000,0.442800 4540000,0.487000 4550000,0.507700 4560000,0.509600 4570000,0.444600 4580000,0.531600 4590000,0.512300 4600000,0.504500 4610000,0.535600 4620000,0.546600 |
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 |
---|---|
ggcskew | Calculates the GC skew of the input sequence |
ggeneskew | Calculate the gene strand bias of the given genome |
ggenomicskew | Calculates the GC skew in different regions of the given genome |
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