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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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2010
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| Online Access: | http://hdl.handle.net/1721.1/60217 https://orcid.org/0000-0001-8253-7714 https://orcid.org/0000-0002-2724-7228 |
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| author | Devadas, Srinivas Waldispuhl, Jerome Berger, Bonnie Clote, Peter |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Devadas, Srinivas Waldispuhl, Jerome Berger, Bonnie Clote, Peter |
| author_sort | Devadas, Srinivas |
| collection | MIT |
| 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/. |
| first_indexed | 2024-09-23T13:10:35Z |
| format | Article |
| id | mit-1721.1/60217 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:10:35Z |
| publishDate | 2010 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/602172022-04-06T12:55:54Z RNAmutants: a web server to explore the mutational landscape of RNA secondary structures Devadas, Srinivas Waldispuhl, Jerome Berger, Bonnie Clote, Peter Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Department of Mathematics Devadas, Srinivas Devadas, Srinivas Waldispuhl, Jerome Berger, Bonnie 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/. National Science Foundation (U.S.) (DBI-0543506) (DMS- 0817971) 2010-12-06T22:54:18Z 2010-12-06T22:54:18Z 2009-06 2009-05 Article http://purl.org/eprint/type/JournalArticle 0305-1048 http://hdl.handle.net/1721.1/60217 Waldispühl, Jerome et al. “RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.” Nucleic Acids Research 37.suppl 2 (2009): W281 -W286. https://orcid.org/0000-0001-8253-7714 https://orcid.org/0000-0002-2724-7228 en_US http://dx.doi.org/10.1093/nar/gkp477 Nucleic Acids Research Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/ application/pdf Oxford University Press MIT web domain |
| spellingShingle | Devadas, Srinivas Waldispuhl, Jerome 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 |
| url | http://hdl.handle.net/1721.1/60217 https://orcid.org/0000-0001-8253-7714 https://orcid.org/0000-0002-2724-7228 |
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