psiblast runs PSI-BLAST given scopalign alignments.

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 (

Here is a sample session with psiblast:

% psiblasts

Mandatory qualifiers:

[-align] (string)

Location of alignment files for input.

[-alignextn] (string)

File extension of alignment files.

[-niter] (integer)

Number of PSI-BLAST 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.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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