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 nameDescription
contactsReads coordinate files and writes contact files
dichetParse dictionary of heterogen groups
interfaceReads coordinate files and writes inter-chain contact files
psiblastsRuns PSI-BLAST given scopalign alignments
scopalignGenerate alignments for SCOP families
siggenGenerates a sparse protein signature
sigscanScans 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