Reverse Position-Specific BLAST. A program used to identify conserved domains in a protein query sequence. It does this by comparing a query protein sequence to position-specific score matrices (PSSM)s that have been prepared from conserved domain alignments. RPS-BLAST is a “reverse” version of position-specific iterated BLAST (PSI-BLAST); however, RPS-BLAST compares a query sequence against a database of profiles prepared from ready-made alignments, whereas PSI-BLAST builds alignments starting from a single protein sequence.