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935 B
Text
20 lines
935 B
Text
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HMMER: biosequence analysis using profile hidden Markov models
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HMMER is used for searching sequence databases for sequence homologs,
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and for making sequence alignments. It implements methods using
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probabilistic models called profile hidden Markov models (profile HMMs).
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HMMER is often used together with a profile database, such as Pfam or
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many of the databases that participate in Interpro. But HMMER can also
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work with query sequences, not just profiles, just like BLAST. For
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example, you can search a protein query sequence against a database with
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phmmer, or do an iterative search with jackhmmer.
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HMMER is designed to detect remote homologs as sensitively as possible,
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relying on the strength of its underlying probability models. In the
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past, this strength came at significant computational expense, but as
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of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
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Publications:
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http://hmmer.org/publications.html
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