hmmer

Build profile HMMs and scan sequences against databases

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Build profile HMMs and scan against sequence databases

hmmbuildhmmsearchhmmscanhmmpresshmmfetchhmmstathmmemithmmconverthmmalign

Build a Hidden Markov Model from a multiple sequence alignment$ hmmbuild output.hmm input_alignment.sto

Search a protein sequence database for matches to an HMM profile$ hmmsearch --tblout results.txt myprofile.hmm protein_db.fasta

Scan a sequence against a collection of HMM profiles$ hmmscan --domtblout domain_results.txt Pfam-A.hmm query_sequence.fasta