gaaui

 

Function

Calculates various indece of amino acid usage

Description

gaaui calculates amino acid usage indices for proteins (excluding
formylmethionine). Calculated indices are as follows,
Laa: Length in amino acids
ndaa: Number of different amino acids
Haau: Entropy of amino acid usage
mmw: Mean molecular weight
gravy: Mean hydropathic indices of each amino acid
aroma: Relative frequency of aromatic amino acids

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 gaaui 

% gaaui refseqn:NC_000913
Calculates various indece of amino acid usage
AAINDEX entry output file [nc_000913.gaaui]:
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 AAINDEX entry output file Output file <*>.gaaui
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-[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

gaaui reads one or more nucleotide sequences.

Output file format

The output from gaaui is to a plain text file.

File: nc_000913.gaaui

Sequence: NC_000913
Laa,ndaa,Haau,mmw,gravy,aroma,gene
20,8,2.4842,117.48,+0.0150,0.0000,thrL
819,20,4.0887,126.65,+0.0328,0.0659,thrA
309,20,4.1228,126.35,+0.0181,0.0712,thrB
427,20,4.0806,128.00,-0.1014,0.0843,thrC
97,18,3.9165,133.54,-1.0268,0.0928,yaaX
257,19,4.0733,132.55,-0.4117,0.1089,yaaA
475,20,4.0413,126.46,+0.6781,0.1242,yaaJ
316,20,4.0395,128.99,-0.2165,0.0728,talB

[Part of this file has been deleted for brevity]

169,20,4.0001,124.90,+0.0231,0.0710,yjjX
214,20,3.9937,129.77,-0.3813,0.0374,ytjC
288,20,4.1421,132.58,-0.3628,0.1111,rob
156,20,4.0627,126.72,-0.0442,0.0705,creA
228,20,4.0471,131.94,-0.1408,0.0789,creB
473,20,4.0254,128.01,+0.0023,0.0677,creC
449,20,4.0871,128.66,+0.2082,0.0980,creD
237,20,4.0729,132.54,-0.4970,0.0675,arcA
45,15,3.5800,123.27,+0.7533,0.0222,yjjY
227,20,4.0283,128.63,-0.0031,0.0573,yjtD


Data files

None.

Notes

None.

References

   Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and
      aromaticity are the major trends of amino-acid usage in 999 Escherichia
      coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a

   Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga
      maritima J Mol Evol. 54(5):563-8.

   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
gaminoinfo Prints out basic amino acid sequence statistics
gcodoncompiler Calculate various kinds of amino acid and codon usage data

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.