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ggcskew |
ggcskew calculates and plots the GC skew of the given sequence. The "skew"
of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can
alternatively calculate AT skew, purine skew, and keto skew, as well as
cumulative skew. GC skew is used to observe various biological aspects
such as prediction of replication origin and terminus in bacteria.
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/
% ggcskew refseqn:NC_000913 Calculates the GC skew of the input sequence Program compseq output file (optional) [nc_000913.ggcskew]: |
% ggcskew refseqn:NC_000913 -plot -graph png Calculates the GC skew of the input sequence Created ggcskew.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 | <*>.ggcskew |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-window | integer | Window size to observe | Any integer value | 10000 |
-slide | integer | Window slide size | Any integer value | 10000 |
-cumulative | boolean | Include to calculate cumulative skew | Boolean value Yes/No | No |
-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 | 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
ggcskew reads one or more nucleotide sequences.
The output from ggcskew is to a plain text file or the EMBOSS graphics device.
File: nc_000913.ggcskew
Sequence: NC_000913 location,GC skew 0,-0.035529 10000,-0.039648 20000,-0.049791 30000,0.005072 40000,-0.063483 50000,-0.030256 60000,0.011875 70000,-0.029478 [Part of this file has been deleted for brevity] 4530000,-0.017164 4540000,-0.036140 4550000,-0.028166 4560000,0.012166 4570000,-0.040486 4580000,-0.020692 4590000,-0.043920 4600000,-0.026363 4610000,-0.022778 4620000,-0.049396 |
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 |
---|---|
ggcwin | Calculates the GC content along the given genome |
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