hmmsearch
hmmsearch is a command-line program used for searching protein sequence databases for homologous sequences using a profile hidden Markov model (HMM). It is part of the HMMER suite of tools, developed by the Lawrence Berkeley National Laboratory. The program takes an HMM profile as input, which represents a set of related proteins, and scans a target database for sequences that match the profile. This allows for the identification of proteins that are evolutionarily related to the query set, even if they have diverged significantly in sequence.
The primary function of hmmsearch is to find remote homologs, meaning proteins that share a common ancestor
hmmsearch works by comparing each sequence in the target database against the HMM profile. It calculates a