SCANPS implements local alignment methods [Smith & Waterman, 1981,Barton, 1993a] for protein and nucleic acid sequence database searching. The program has been made to run efficiently in parallel on Silicon Graphics hardware. A WWW server that allows searching of the SWALL non-redundant database of protein sequences is available at the EBI on http://www2.ebi.ac.uk/scanps/. Alternative software is the SSEARCH program that is distributed in the FASTA package from W. Pearson (ftp://ftp.virginia.edu).