gbui

 

Function

Calculates base usage indices for protein-coding sequences

Description

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/

Usage

Here is a sample session with gbui

% gbui refseqn:NC_000913
Calculates base usage indices for protein-coding sequences
Program compseq output file [nc_000913.gbui]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

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 (Assess overall base usage of the gene)
1 (Assess base usage at 1st position of codons)
2 (Assess base usage at 2nd position of codons)
3 (Assess base usage at 3rd position of codons)
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

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gbui reads one or more nucleotide sequences.

Output file format

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

Data files

None.

Notes

None.

References

   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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
gdinuc Calculates dinucleotide usage

Author(s)

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

History

2012 - Written by Hidetoshi Itaya

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scrips.

Comments

None.