Position-Specific Iterated BLAST. PSI-BLAST (Altschul et al., J Mol Biol 215:403-410; 1990) is used for iterative protein–sequence similarity searches using a position-specific score matrix (PSSM). It is a program for searching protein databases using protein queries to find other members of the same protein family. All statistically significant alignments found by BLAST are combined into a multiple alignment, from which a PSSM is constructed. This matrix is used to search the database for additional significant alignments, and the process may be iterated until no new alignments are found.