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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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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 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.gaaui] AAINDEX entry output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -[no]accid boolean [Y] Include to use sequence accession ID as query Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit 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 gaminoinfo Prints out basic amino acid sequence statistics gbui Calculates base usage indeces for protein-codin sequences gcodoncompiler Calculates 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 2013 - Fixed by Hidetoshi Itaya Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None.