--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/doc/text/gaminoinfo.txt	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,219 @@
+                                   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.
+