What is SCANPS?

SCANPS is a program for comparing a protein sequence to a database of sequences. It has the following features:

1. Full Smith-Waterman style searching with a single sequence.

2. Multiple domain matches found against each database sequence.

3. Iterative profile searching similar in concept to PSI-BLAST, but with full dynamic programming on each cycle for additional sensitivity.

4. Significance of matches calculated ``on the fly'' for each search.

5. Efficient implementation on Intel CPUs by using MMX and SSE instructions.

6. Output of each search as pairwise alignments and multiple alignments.