seqsort

 

Function

Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file

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
*  -psipath            string     Location of scop hits files (input)
*  -psiextn            string     Extension of scop hits files
*  -swisspath          string     Location of seqwords hits files
*  -swissextn          string     Extension of seqwords input files
*  -psifile            string     Name of file containing processed scop hits
                                  file (input)
*  -swissfile          string     Name of file containing processed seqwords
                                  hits file (input)
   -overlap            integer    number of overlapping residues required for
                                  merging of two hits
  [-hitsf]             outfile    Name of scop hits file (output)
  [-validf]            outfile    Name of validation file (output)

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


Mandatory qualifiers Allowed values Default
-mode Select mode
1 (Process psiblast hits)
2 (Process swissparse hits)
3 (Merge psiblast and swissparse hits)
1
-psipath Location of scop hits files (input) Any string is accepted ./
-psiextn Extension of scop hits files Any string is accepted .hits
-swisspath Location of seqwords hits files Any string is accepted ./
-swissextn Extension of seqwords input files Any string is accepted .swissparse
-psifile Name of file containing processed scop hits file (input) Any string is accepted An empty string is accepted
-swissfile Name of file containing processed seqwords hits file (input) Any string is accepted An empty string is accepted
-overlap number of overlapping residues required for merging of two hits Any integer value 10
[-hitsf]
(Parameter 1)
Name of scop hits file (output) Output file seqsort.fam
[-validf]
(Parameter 2)
Name of validation file (output) Output file seqsort.all
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 files of intra-chain residue-residue contact data
dichetParse dictionary of heterogen groups
hmmgenGenerates a hidden Markov model for each alignment in a directory
interfaceReads coordinate files and writes files of inter-chain residue-residue contact data
profgenGenerates various profiles for each alignment in a directory
psiblastsRuns PSI-BLAST given scopalign alignments
scopalignGenerate alignments for families in a scop classification file by using STAMP
scoprepReorder scop classificaiton file so that the representative structure of each family is given first
scopresoRemoves low resolution domains from a scop classification file
seqalignGenerate extended alignments for families in a scop families file by using CLUSTALW with seed alignments
seqsearchGenerate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments
seqwordsGenerate file of hits for scop families by searching swissprot with keywords
siggenGenerates a sparse protein signature from an alignment and residue contact data
sigscanScans a signature against swissprot and writes a signature hits files

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