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nhmmer: DNA homology search with profile HMMs

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 applie...

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Detalles Bibliográficos
Autores principales: Wheeler, Travis J., Eddy, Sean R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777106/
https://www.ncbi.nlm.nih.gov/pubmed/23842809
http://dx.doi.org/10.1093/bioinformatics/btt403
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author Wheeler, Travis J.
Eddy, Sean R.
author_facet Wheeler, Travis J.
Eddy, Sean R.
author_sort Wheeler, Travis J.
collection PubMed
description 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. Contact: wheelert@janelia.hhmi.org
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spelling pubmed-37771062013-09-22 nhmmer: DNA homology search with profile HMMs Wheeler, Travis J. Eddy, Sean R. Bioinformatics Applications Notes 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. Contact: wheelert@janelia.hhmi.org Oxford University Press 2013-10-01 2013-07-09 /pmc/articles/PMC3777106/ /pubmed/23842809 http://dx.doi.org/10.1093/bioinformatics/btt403 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Wheeler, Travis J.
Eddy, Sean R.
nhmmer: DNA homology search with profile HMMs
title nhmmer: DNA homology search with profile HMMs
title_full nhmmer: DNA homology search with profile HMMs
title_fullStr nhmmer: DNA homology search with profile HMMs
title_full_unstemmed nhmmer: DNA homology search with profile HMMs
title_short nhmmer: DNA homology search with profile HMMs
title_sort nhmmer: dna homology search with profile hmms
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777106/
https://www.ncbi.nlm.nih.gov/pubmed/23842809
http://dx.doi.org/10.1093/bioinformatics/btt403
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