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 but may have low sequence identity. It achieves this by using the probabilistic nature of HMMs, which capture conserved patterns of amino acids and their probabilities of occurrence at specific positions within a protein family. This makes it a powerful tool for protein family classification, annotation, and functional prediction.

hmmsearch works by comparing each sequence in the target database against the HMM profile. It calculates a score for each comparison, indicating the likelihood that the sequence is a member of the protein family represented by the HMM. Sequences exceeding a predefined significance threshold are reported as potential homologs. The output typically includes the sequence identifier, the score, and other relevant statistical information. The program is widely used in bioinformatics research for exploring protein evolution and function.