An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptim

Background: RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm) for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best exami...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Alexander Churkin, Danny Barash
• Keywords: BMCBI 2008, Mutations, Point Mutations, Secondary Structure