gaminoinfo

 

Function

Prints out basic amino acid sequence statistics

Description

gaminoinfo prints out basic compositional statistics of the given amino
acid sequence in a human readble manner. The calculated values are molecular
weight, number of residues, average residue weight, charge, isoelectric
point, number/mole/Dayhoffstat of each amino acid, and percentage of
Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),
Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),
Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and
Acidic (B+D+E+Z) reidues.


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 gaminoinfo

% gaminoinfo tsw:hbb_human
Prints out basic amino acid sequence statistics
AAINDEX entry output file [hbb_human.gaminoinfo]: 

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 Protein sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-outfile]
(Parameter 2)
outfile AAINDEX entry output file Output file <*>.gaminoinfo
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

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

gaminoinfo reads one or more protein sequences.

Output file format

The output from gaminoinfo is to a plain text file.

File: hbb_human.gaminoinfo

Sequence: P68871
AminoInfo of from 1 to 158

Molecular weight = 19309.27 Residues = 158
Average Weight = 122.21 Charge = 3.5
Isoelectric Point = 7.4065
Residue Number Mole% DayhoffStat

= 1 0.633 0.000
> = 1 0.633 0.000
A = Ala 16 10.127 1.178
B = Asx 2 1.266 0.000
C = Cys 2 1.266 0.436
D = Asp 7 4.430 0.806
E = Glu 8 5.063 0.844
F = Phe 8 5.063 1.406
G = Gly 13 8.228 0.980
H = His 11 6.962 3.481
K = Lys 11 6.962 1.055
L = Leu 18 11.392 1.540
M = Met 3 1.899 1.117
N = Asn 7 4.430 1.030
P = Pro 7 4.430 0.852
Q = Gln 3 1.899 0.487
R = Arg 3 1.899 0.387
S = Ser 5 3.165 0.452
T = Thr 7 4.430 0.726
U = Sec 1 0.633 0.000
V = Val 18 11.392 1.726
W = Trp 2 1.266 0.974
Y = Tyr 3 1.899 0.558
_ = 1 0.633 0.000

Property Residues Number Mole%
Tiny (A+C+G+S+T) 43 27.215
Small (A+B+C+D+G+N+P+S+T+V) 84 53.165
Aliphatic (I+L+V) 36 22.785
Aromatic (F+H+W+Y) 24 15.190
Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962
Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241
Charged (B+D+E+H+K+R+Z) 42 26.582
Basic (H+K+R) 25 15.823
Acidic (B+D+E+Z) 17 10.759

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
gaaui Calculates various indece of amino acid usage
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.