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gbui |
gbui calculates base usage indices of protein-coding sequences (excluding
start and stop codons) for each gene. Indices calculated are as follows,
acgt: Total bumber of bases (A+T+G+C)
ryr: Purine/Pyrimidine ratio (A+G)/(T+C)
gcc: G+C content (G+C)/(A+T+G+C)
Hgc: entropy of G+C content (G+C)/(A+T+G+C)
gcs: GC skew (C-G)/(C+G)
ats: AT skew (A-T)/(A+T)
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/
% gbui refseqn:NC_000913 Calculates base usage indices for protein-coding sequences Program compseq output file [nc_000913.gbui]: |
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 | <*>.gbui | ||||||||
Additional (Optional) qualifiers | ||||||||||||
(none) | ||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||
-translate | boolean | Include when translating using standard codon table | Boolean value Yes/No | No | ||||||||
-position | list | Codon position |
|
all | ||||||||
-delkey | string | Regular expression to delete key | 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
gbui reads one or more nucleotide sequences.
The output from gbui is to a plain text file.
File: nc_000913.gbui
Sequence: NC_000913 acgt,ryr,gcc,Hgc,gcs,ats,gene 60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL 2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA 927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB 1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC 291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX 771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA 1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ 948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB [Part of this file has been deleted for brevity] 507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX 642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC 864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob 468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA 684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB 1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC 1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD 711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA 135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY 681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD |
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 |
---|---|
gdinuc | Calculates dinucleotide usage |
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