nhmmer: DNA homology search with profile HMMs | Zendy

Travis J. Wheeler | Zendy; Sean R. Eddy | Zendy

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nhmmer: DNA homology search with profile HMMs

Author(s) -

Travis J. Wheeler,

Sean R. Eddy

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt403

Subject(s) - annotation , homology (biology) , computer science , computational biology , genome project , inference , genome , dna , source code , sequence homology , dna sequencing , hidden markov model , biology , programming language , genetics , base sequence , artificial intelligence , gene

Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome.

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