
                             EMBOSS: psiblasts
     _________________________________________________________________
   
                               Program psiblasts
                                       
Function

   Runs PSI-BLAST given scopalign 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 psiblasts:

% psiblasts

Command line arguments

   Mandatory qualifiers:
  [-align]             string     Location of alignment files for input
  [-alignextn]         string     File extension of 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
  [-families]          outfile    Name of families file for output
  [-logf]              outfile    Name of log file for the build

   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
   [-align]
   (Parameter 1) Location of alignment files for input Any string is
   accepted ./
   [-alignextn]
   (Parameter 2) File extension of alignment files Any string is accepted
   .align
   [-niter]
   (Parameter 3) Number of PSIBLAST iterations Any integer value 1
   [-evalue]
   (Parameter 4) Threshold E-value for inclusion in family Any integer
   value 0.001
   [-maxhits]
   (Parameter 5) Maximum number of hits Any integer value 1000
   [-submatrix]
   (Parameter 6) Residue substitution matrix Any string is accepted
   ./EBLOSUM62
   [-families]
   (Parameter 7) Name of families file for output Output file scop.hits
   [-logf]
   (Parameter 8) Name of log file for the build Output file psiblasts.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 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
   scopalign Generate alignments for SCOP families
   seqsort Removes ambiguities from a set of hits resulting from a
   database search
   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
