
                              EMBOSS: seqsort
     _________________________________________________________________
   
                                Program seqsort
                                       
Function

   Removes ambiguities from a set of hits resulting from a database
   search
   
Description

   This is part of Jon Ison's protein structure analysis package.
   
   This package is still being developed.
   
   Please ignore this program until further details can be documented.
   
   All further queries should go to Jon Ison. (Jon Ison)
   
Usage

   Here is a sample session with seqsort:

% seqsort

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-mode]              menu       Select mode
  [-overlap]           integer    number of overlapping residues required for
                                  merging of two hits
*  -psipath            string     Location of psiblasts hits files
*  -psiextn            string     Extension of psiblasts hits files
*  -swisspath          string     Location of swissparse hits files
*  -swissextn          string     Extension of swissparse input files
*  -psifile            string     Name of file containing sorted psiblasts
                                  results
*  -swissfile          string     Name of file containing sorted swissparse
                                  results
  [-outfile]           string     Name of output file

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-mode]
   (Parameter 1) Select mode
   1 (Process psiblast hits)
   2 (Process swissparse hits)
   3 (Merge psiblast and swissparse hits)
   1
   [-overlap]
   (Parameter 2) number of overlapping residues required for merging of
   two hits Any integer value 10
   -psipath Location of psiblasts hits files Any string is accepted ./
   -psiextn Extension of psiblasts hits files Any string is accepted
   .psiblasts
   -swisspath Location of swissparse hits files Any string is accepted ./
   -swissextn Extension of swissparse input files Any string is accepted
   .swissparse
   -psifile Name of file containing sorted psiblasts results Any string
   is accepted An empty string is accepted
   -swissfile Name of file containing sorted swissparse results Any
   string is accepted An empty string is accepted
   [-outfile]
   (Parameter 3) Name of output file Any string is accepted An empty
   string is accepted
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

Output file format

Data files

Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                         Description
   contacts     Reads coordinate files and writes contact files
   dichet       Parse dictionary of heterogen groups
   interface    Reads coordinate files and writes inter-chain contact files
   psiblasts    Runs PSI-BLAST given scopalign alignments
   scopalign    Generate alignments for SCOP families
   siggen       Generates a sparse protein signature
   sigscan      Scans a sparse protein signature against swissprot
   
Author(s)

   This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)
   
History

   Written (date) - author.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
