seqsearch generate files of hits for families in a scop classification file by using PSI-BLAST with seed 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 ([email protected]).

Here is a sample session with seqsearch:

% seqsearch

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 PSI-BLAST 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.