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gaminoinfo |
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/
% gaminoinfo tsw:hbb_human Prints out basic amino acid sequence statistics AAINDEX entry output file [hbb_human.gaminoinfo]: |
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) |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gaminoinfo reads one or more protein sequences.
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 |
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 |
---|---|
gaaui | Calculates various indece of amino acid usage |
gcodoncompiler | Calculate various kinds of amino acid and codon usage data |
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