OVERVIEW
HMMER
HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called 'profile hidden Markov models' (profile HMMs). HMMER is used by many protein family domain databases and large-scale annotation pipelines, including Pfam and other members of the InterPro Consortium.
HMMER offcial site: http://hmmer.org/