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PMID: 23842809 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

nhmmer: DNA homology search with profile HMMs.

Bioinformatics (Oxford, England) ·Vol. 29 ·No. 19 ·2013-10-01 ·Pages 2487-9

Wheeler TJ, Eddy SR

Abstract

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. 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.

MeSH Terms
Algorithms DNA/analysis DNA Transposable Elements Genome, Human Humans Markov Chains Probability Sequence Alignment Sequence Homology, Nucleic Acid Software
Chemicals
DNA Transposable Elements DNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Wheeler Travis J
HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.
Eddy Sean R
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Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btt403
Published
2013-10-01
Epub
2013-00-09
Pages
2487-9
Language
English
Region
England
NLM ID
9808944
PMCID
PMC3777106
Subset
IM
Grants
Howard Hughes Medical Institute · United States
External Links
PubMed source DOI: 10.1093/bioinformatics/btt403 PMC Full Text View journal details
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