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gnucleotideperiodicity |
gnucleotideperiodicity checks the periodicity of certain nucleotide
(best known with AA dinucleotide). Bacteria and archaebacteria are
known to show periodicity of ApA dinucleotides at about 11bp and 10bp.
Lower eukaryotes also show periodicity but higher eukaryotes do not.
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/
% gnucleotideperiodicity refseqn:NC_000913 Checks the periodicity of certain oligonucleotides Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]: |
? % gnucleotideperiodicity refseqn:NC_000913 -plot -graph png Checks the periodicity of certain oligonucleotides Created gnucleotideperiodicity.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 | <*>.gnucleotideperiodicity |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-format | string | Output file format. Dependent on 'convert' command | Any string | png |
-window | integer | Window size to seek periodicity | Any integer value | 50 |
-nucleotide | string | Nucleotide to search | Any string | aa |
-[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
gnucleotideperiodicity reads one or more nucleotide sequences.
The output from gnucleotideperiodicity is to a plain text file or the EMBOSS graphics device.
File: nc_000913.gnucleotideperiodicity
Sequence: NC_000913 window,value 0,35134 1,30121 2,25409 3,23508 4,25830 5,25136 6,25658 7,28279 [Part of this file has been deleted for brevity] 40,28042 41,25892 42,25968 43,28240 44,25841 45,25591 46,27788 47,25832 48,25427 49,0 |
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 |
---|---|
gkmertable | Create an image showing all k-mer abundance within a sequence |
goligomercounter | Counts the number of given oligomers in a sequence |
goligomersearch | Searches oligomers in given sequence |
gsignature | Calculate oligonucleotide usage (genomic signature) |
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