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gviewcds |
gviewcds creates a graph showing the average A,T,G,C contents
around start/stop codons. This is useful to view consensus around
start/stop codons and to find characteristic pattern in CDS.
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/
Here is a sample session with gviewcds % gviewcds refseqn:NC_000913 Displays a graph of nucleotide contents around start and stop codons Program compseq output file (optional) [nc_000913.gviewcds]: |
% gviewcds refseqn:NC_000913 -plot -graph png Displays a graph of nucleotide contents around start and stop codons Created gviewcds.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 | <*>.gviewcds |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-length | integer | Length in bases to show around start/stop codons | Any integer value | 100 |
-gap | integer | Gap shown in graph in between start/stop codon neighbors | Any integer value | 3 |
-[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
gviewcds reads one or more nucleotide sequences.
The output from gviewcds is to a plain text file or the EMBOSS graphics device.
File: nc_000913.gviewcds
Sequence: NC_000913 position,A,T,G,C 1,28.20,27.60,22.18,22.02 2,26.05,26.81,23.06,24.08 3,27.34,27.37,23.94,21.35 4,26.28,28.83,23.01,21.88 5,26.72,28.22,22.18,22.88 6,26.42,26.72,24.96,21.90 7,27.21,28.66,21.95,22.18 8,25.47,28.39,23.06,23.08 [Part of this file has been deleted for brevity] 400,26.60,27.44,22.67,23.27 401,24.38,26.63,25.05,23.92 402,25.03,26.37,23.71,24.87 403,25.96,27.53,22.53,23.96 404,26.63,25.52,24.17,23.66 405,25.68,26.26,23.50,24.54 406,24.94,26.86,23.92,24.26 407,25.54,26.28,23.73,24.43 408,25.28,26.93,24.38,23.39 409,26.63,26.46,22.32,24.57 |
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 |
---|---|
gbasecounter | Creates a position weight matrix of oligomers around start codon |
gbasezvalue | Extracts conserved oligomers per position using Z-score |
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