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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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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 |
format | Online Article Text |
id | pubmed-3777106 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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