nhmmer

nhmmer is a command-line program used for sequence similarity searching. It is part of the HMMER software package, which is designed for searching biological sequence databases using profile hidden Markov models (profile HMMs). Profile HMMs are statistical models that represent a family of related protein or nucleotide sequences, capturing conserved patterns and evolutionary relationships.

The primary function of nhmmer is to compare a query sequence against a database of profile HMMs. This allows researchers to identify sequences that are likely to belong to a particular protein family or to find homologous sequences to a known protein. nhmmer is particularly effective at detecting distant evolutionary relationships that might be missed by simpler alignment methods like BLAST.

The program works by scoring the query sequence against each profile HMM in the database. Sequences that achieve a score above a certain threshold are considered significant matches. nhmmer can be used for tasks such as protein domain annotation, gene family analysis, and identifying potential functional sites within a sequence. It is widely used in bioinformatics and computational biology for large-scale sequence analysis and discovery.