SCANPS (pronounced Scan-P-S) stands for SCAN Protein Sequence. The main function of SCANPS is to use a rigorous local alignment method to search protein sequence databases with a query sequence or multiple alignment. SCANPS also allows all pairwise comparsons to be made between a set of sequences and can estimate the statistical significance of the alignments. SCANPS has been used in the analysis of many protein families. For example, it was used to make the discovery of similarity between PD-ECGF (Platelet derived endothelial cell growth factor) and TP (Thymidine Phosphorylase) [4]. The program was also used to find the similarity between E. coli diadenosine tetra-phosphatase and the protein Ser/Thr phosphatases [3].