Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gaminoinfo.txt @ 2:8947fca5f715 draft default tip
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| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:21:44 -0400 |
| parents | 84a17b3fad1f |
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--- a/GEMBASSY-1.0.3/doc/text/gaminoinfo.txt Fri Jun 26 05:20:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,219 +0,0 @@ - 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. -