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RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, Cl...

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Detalles Bibliográficos
Autores principales: Waldispühl, Jerome, Devadas, Srinivas, Berger, Bonnie, Clote, Peter
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703890/
https://www.ncbi.nlm.nih.gov/pubmed/19531740
http://dx.doi.org/10.1093/nar/gkp477
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author Waldispühl, Jerome
Devadas, Srinivas
Berger, Bonnie
Clote, Peter
author_facet Waldispühl, Jerome
Devadas, Srinivas
Berger, Bonnie
Clote, Peter
author_sort Waldispühl, Jerome
collection PubMed
description The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/.
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spelling pubmed-27038902009-07-01 RNAmutants: a web server to explore the mutational landscape of RNA secondary structures Waldispühl, Jerome Devadas, Srinivas Berger, Bonnie Clote, Peter Nucleic Acids Res Articles The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. Oxford University Press 2009-07-01 2009-06-16 /pmc/articles/PMC2703890/ /pubmed/19531740 http://dx.doi.org/10.1093/nar/gkp477 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Waldispühl, Jerome
Devadas, Srinivas
Berger, Bonnie
Clote, Peter
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title_full RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title_fullStr RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title_full_unstemmed RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title_short RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
title_sort rnamutants: a web server to explore the mutational landscape of rna secondary structures
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703890/
https://www.ncbi.nlm.nih.gov/pubmed/19531740
http://dx.doi.org/10.1093/nar/gkp477
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