Nucleic Acids Research Advance Access originally published online on June 16, 2009
Nucleic Acids Research 2009 37(Web Server issue):W281-W286; doi:10.1093/nar/gkp477
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W281-W286
© 2009 The Author(s)
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.
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RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
1Department of Mathematics, 2Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, 3Electrical Engineering and Computer Science, MIT, Cambridge and 4Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
*To whom correspondence should be addressed. Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu Correspondence may also be addressed to Bonnie Berger. Tel: +1 617 253 1827; Fax: +1 617 258 5429; Email: bab{at}mit.edu
Received February 26, 2009. Revised May 6, 2009. Accepted May 17, 2009.
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/.