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ggenomicskew |
ggenomicskew calculates and plots the GC skew for the whole genome, coding
regions, intergenic regions, and the third codon. This program is useful in
visualizing various base composition bias within the genome. AT skew can be
calculated instead of GC skew by toggling the -at qualifier.
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/
% ggenomicskew refseqn:NC_000913 Calculates the GC skew in different regions of the given genome Program compseq output file (optional) [nc_000913.ggenomicskew]: |
% ggenomicskew refseqn:NC_000913 -plot -graph png Calculates the GC skew in different regions of the given genome Created ggenomicskew.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 | <*>.ggenomicskew |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-divide | integer | Window to divide into | Any integer value | 250 |
-at | boolean | Input 1 when observing AT skew instead of GC skew | 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
ggenomicskew reads one or more nucleotide sequences.
The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.
File: nc_000913.ggenomicskew
Sequence: NC_000913 location,GC skew,coding,intergenic,third codon 0,-0.036259,-0.040085,-0.034707,-0.141888, 1,-0.031167,-0.035657,0.047953,-0.175758, 2,-0.028670,-0.031139,-0.049143,-0.018466, 3,-0.016647,-0.004656,-0.102616,0.086181, 4,-0.041985,-0.029846,-0.088670,0.015291, 5,-0.097093,-0.103813,-0.067275,-0.247401, 6,-0.028028,-0.016363,-0.048806,-0.047332, 7,-0.055805,-0.059329,-0.020071,-0.123271, [Part of this file has been deleted for brevity] 241,0.000772,-0.012151,-0.063786,0.069585, 242,-0.025787,-0.000384,-0.049143,0.029431, 243,0.010516,0.008217,-0.030600,0.128657, 244,-0.037115,-0.015134,0.017500,0.035398, 245,-0.000317,0.006021,-0.047170,0.091549, 246,-0.025417,-0.015190,-0.116608,0.044619, 247,-0.038404,-0.035676,-0.135714,0.015375, 248,-0.026246,-0.024240,-0.037190,-0.130118, 249,-0.053371,-0.057225,-0.022472,-0.082167, 250,-0.026316,0.166667,-0.151515,0.000000, |
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 |
ggeneskew | Calculate the gene strand bias 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