--- 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.
-