| ## 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