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ggeneskew |
ggeneskew calculates and plots the strand bias of genes (or the GC skew
within them). By default, this program visualizes the gene strand preference
(1 for direct, -1 for complement strand), but by specifying -base option
option, GC/AT/Purine/Keto skews of the coding regions or more specifically
in the GC3 (third codon position) with -gctri option can be calculated.
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/
% ggeneskew refseqn:NC_000913 Calculate the gene strand bias of the given genome Program compseq output file (optional) [nc_000913.ggeneskew]: |
% ggeneskew refseqn:NC_000913 -plot -graph png Calculate the gene strand bias of the given genome Created ggeneskew.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 | <*>.ggeneskew |
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 | Input 1 to calculate cumulative skew | Boolean value Yes/No | No |
-base | selection | Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews | Choose from selection list of values | none |
-gctri | boolean | Include to use only the third codon positions | Boolean value Yes/No | No |
-[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
ggeneskew reads one or more nucleotide sequences.
The output from ggeneskew is to a plain text file or the EMBOSS graphics device.
File: nc_000913.ggeneskew
Sequence: NC_000913 location,gene None skew 190,0.294118 337,-0.058914 2801,-0.120000 3734,-0.070588 5234,0.037500 5683,0.020725 6529,0.032765 8238,-0.028226 [Part of this file has been deleted for brevity] 4631820,-0.093407 4632464,-0.006479 4633544,-0.120690 4634030,-0.060367 4634719,-0.104167 4636201,-0.144560 4637613,0.010929 4638425,0.200000 4638965,-0.081871 , |
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 |
ggcwin | Calculates the GC content along 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