Consensus RNA Secondary Structure Prediction by Ranking k-Length Stems

The accurate computational prediction of RNA secondary structures is a difficult task, but an important one, since RNA structure is usually more evolutionarily conserved than primary sequence. We describe a dynamic programming algorithm called FoldRRS (Folding of RNA by Ranking of Stems) that predicts a consensus secondary structure from a multiple sequence alignment. Our algorithm exploits the use of k-length stems (k = 2) to acquire base pairing probability and covariation information from individual sequences. We test sequences from the BRAliBase I data set [1] and the Rfam database [2]. Our results were compared against three algorithms, RNAalifold, Pfold, and KNetFold, that are similar in nature. FoldRRS exhibits an increase in accuracy over the other programs in data sets which contain longer and/or more numerous sequences.

• Type: Conference
• Year: 2009
• Where: BIOCOMP
• Authors: Denise Y. F. Mak, Gary Benson
• Keywords: BIOCOMP 2007, BIOCOMP 2009, Consensus Secondary Structure, RNA Secondary Structures, Secondary Structure