|Reference||Protein homology detection by HMM-HMM comparison|
|Short Description||Alignment Heuristic|
HHSearch is one of the alignment heuristics. Its goal is to find related sequences. PSI-BLAST improved the search for distant protein family members by introducing position specific scoring matrices. PSSMs are very powerful, but do not contain information about insertions or deletions. HHSearch uses Profile Hidden Markov Models (HMMs), which can encode this information. Therefore HMMs and with them HHSearch can be regarded as the logical next step in the evolution of heuristical alignment methods. HMMs are precalculated for the database. PSI-BLAST is started with the query sequence. The result of PSI-BLAST is converted to a HMM. This HMM is then compared to the HMMs of the database.