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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
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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 Standard (Mandatory) qualifiers: [-sequence] seqall Protein sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.gaminoinfo] AAINDEX entry output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) 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 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 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 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.