nhmmer: DNA homology search with profile HMMs

Bioinformatics. 2013 Oct 1;29(19):2487-9. doi: 10.1093/bioinformatics/btt403. Epub 2013 Jul 9.


Summary: 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.

Availability: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • DNA / analysis*
  • DNA Transposable Elements
  • Genome, Human
  • Humans
  • Markov Chains
  • Probability
  • Sequence Alignment
  • Sequence Homology, Nucleic Acid*
  • Software*


  • DNA Transposable Elements
  • DNA