![]() |
gdinuc |
gdinuc calculates dinucleotide usage indices for protein-coding sequences
(excluding start and stop codons). Dinucleotide usage is computed as the
ratio of observed (O) to expected (E) dinucleotide frequencies within the
given sequence. Dinucleotides are known to have consistent patterns within
the genome (signatures) and tend to have certain periodicities.
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/
% gdinuc refseqn:NC_000913 Calculates dinucleotide usage Program compseq output file [nc_000913.gdinuc]: |
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 | ||||||||
[-outfile] (Parameter 2) |
outfile | Program compseq output file | Output file | <*>.gdinuc | ||||||||
Additional (Optional) qualifiers | ||||||||||||
(none) | ||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||
-translate | boolean | Include when translates using standard codon table | Boolean value Yes/No | No | ||||||||
-position | list | Codon position or reading frame |
|
all | ||||||||
-delkey | string | Regular expression to delete key (i.e. amino acids and nucleotides) | Any string | [^ACDEFGHIKLMNPQRSTVWYacgtU] | ||||||||
-[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gdinuc reads one or more nucleotide sequences.
The output from gdinuc is to a plain text file.
File: nc_000913.gdinuc
Sequence: NC_000913
?
keys,aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,gene, All,1.293,0.921,0.720,1.108,1.022,0.868,1.166,0.925,0.958,1.285,0.897,0.867,0.729,0.891,1.228,1.123, |
None.
None.
Yew et al. (2004) Base usage and dinucleotide frequency of infectious bursal disease virus, Virus Genes, 28:1,41-53. 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 |
---|---|
gbui | Calculates base usage indices for protein-coding sequences |
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