title: corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs.
abstract: RNA molecules can achieve a broad range of regulatory functions through specific structures that are in turn determined by their sequence. The prediction of mutations changing the structural properties of RNA sequences (a.k.a. deleterious mutations) is therefore useful for conducting mutagenesis experiments and synthetic biology applications. While brute force approaches can be used to analyze single-point mutations, this strategy does not scale well to multiple mutations. In this article, we present corRna a web server for predicting the multiple-point deleterious mutations in structural RNAs. corRna uses our RNAmutants framework to efficiently explore the RNA mutational landscape. It also enables users to apply search heuristics to improve the quality of the predictions. We show that corRna predictions correlate with mutagenesis experiments on the hepatitis C virus cis-acting replication element as well as match the accuracy of previous approaches on a large test-set in a much lower execution time. We illustrate these new perspectives offered by corRna by predicting five-point deleterious mutations--an insight that could not be achieved by previous methods. corRna is available at: http://corrna.cs.mcgill.ca.
authors: McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada.
authors: Edmund
authors: E
authors: Lam
authors: Alfred
authors: A
authors: Kam
authors: Jérôme
authors: J
authors: Waldispühl
references: Nat Nanotechnol. 2010 Dec;5(12):833-42
references: 21102465
references: Nano Lett. 2011 Feb 9;11(2):878-87
references: 21229999
references: Curr Protoc Bioinformatics. 2009 Jun;Chapter 12:Unit12.2
references: 19496057
references: PLoS Genet. 2010 Aug 19;6(8):e1001074
references: 20808897
references: Hum Mol Genet. 2006 Oct 15;15 Spec No 2:R162-9
references: 16987879
references: BMC Bioinformatics. 2006 Sep 06;7:404
references: 16956394
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W281-6
references: 19531740
references: Brief Bioinform. 2011 Mar;12(2):104-14
references: 21422070
references: BMC Bioinformatics. 2008 Apr 29;9:222
references: 18445289
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40
references: 18953034
references: J Virol. 2004 Feb;78(3):1352-66
references: 14722290
references: PLoS Comput Biol. 2008 Aug 08;4(8):e1000124
references: 18688270
references: Bioinformatics. 2002;18 Suppl 2:S250-9
references: 12386010
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D280-2
references: 19880381
references: Nucleic Acids Res. 2003 Nov 15;31(22):6578-84
references: 14602917
references: Nat Biotechnol. 2006 May;24(5):545-54
references: 16680139
references: Bioinformatics. 2005 Nov 15;21(22):4140-7
references: 16159920
references: Bioinformatics. 2009 Aug 1;25(15):1974-5
references: 19398448
references: BMC Bioinformatics. 2006 Apr 25;7:221
references: 16638137
references: J Comput Biol. 2011 Nov;18(11):1465-79
references: 22035326
references: Nat Nanotechnol. 2010 Sep;5(9):676-82
references: 20802494