RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
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Devadas_RNAmutants a web.pdf
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3.38 MB
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Adobe PDF
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Author(s)
Devadas, Srinivas
Waldispuhl, Jerome
Berger, Bonnie
Clote, Peter
Date Issued
June 2009
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
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.
Version
Final published version
Abstract
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/.
MIT Department
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
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Attribution Non-Commercial License
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DOI of Published Version
https://doi.org/10.1093/nar/gkp477
