Journal
BIOINFORMATICS
Volume 29, Issue 19, Pages 2487-2489Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt403
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Funding
- Howard Hughes Medical Institute Funding Source: Medline
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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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