seqsearch

 

Function

Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments

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 seqsearch:

% seqsearch

Command line arguments

   Mandatory qualifiers:
  [-escop]             infile     Name of scop classification file (embl
                                  format input)
  [-align]             string     Location of scop alignment files (input)
  [-alignextn]         string     Extension of scop alignment files
   -niter              integer    Number of PSIBLAST iterations
   -evalue             float      Threshold E-value for inclusion in family
   -maxhits            integer    Maximum number of hits
   -submatrix          string     Residue substitution matrix
  [-hits]              string     Location of scop hits files (output)
  [-hitsextn]          string     Extension of scop hits files
   -logf               outfile    Name of log file for the build

   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
[-escop]
(Parameter 1)
Name of scop classification file (embl format input) Input file Escop.dat
[-align]
(Parameter 2)
Location of scop alignment files (input) Any string is accepted ./
[-alignextn]
(Parameter 3)
Extension of scop alignment files Any string is accepted .salign
-niter Number of PSIBLAST iterations Any integer value 1
-evalue Threshold E-value for inclusion in family Any numeric value 0.001
-maxhits Maximum number of hits Any integer value 1000
-submatrix Residue substitution matrix Any string is accepted ./EBLOSUM62
[-hits]
(Parameter 4)
Location of scop hits files (output) Any string is accepted ./
[-hitsextn]
(Parameter 5)
Extension of scop hits files Any string is accepted .hits
-logf Name of log file for the build Output file seqsearch.log
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
seqsortReads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file
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