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gaaui |
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/
% gaaui refseqn:NC_000913 Calculates various indece of amino acid usage AAINDEX entry output file [nc_000913.gaaui]: |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gaaui reads one or more nucleotide sequences.
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 |
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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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
gaminoinfo | Prints out basic amino acid sequence statistics |
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