SSEARCH is a variant of the local dynamic programming algorithm. It provides a rigorous mathematical approach towards sequence alignment using dynamic programming. It is guaranteed to find the best alignment between a pair of sequences given a particular choice of scoring matrix and gap penalties. The Smith-Waterman algorithm searches a database by using local alignments. This allows the database search to focus on the most highly conserved regions of the sequences without having to overcome interference from less well conserved regions of the sequences. It also allows similar domains within sequences to be identified, such as nucleotide binding domains, even though the sequences may not be related over the entire length. The Smith-Waterman algorithm places no restriction on the alignment it reports other than it have a positive score in terms of the similarity table used to score the alignment. It is worth the effort to understand how Smith-Waterman alignments are actually computed. First users should be convinced that the algorithm is mathematically rigorous in sense described here. That it does test all possible alignments, and always does find the best scoring alignment.
SSEARCH uses the same methods to calculate the statistical signifiance of a score as FASTA.