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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.

Geoff Barton (GJB) 2002-07-23