Prediction of Consensus RNA Secondary Structures Including Pseudoknots
Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
IEEE/ACM Trans.\ Comp.\ Biol.\ Bioinf., 1, 66-77, (2004)
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to five different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly, and more than 85% of the base pairs were identified.
RNA secondary structure, pseudoknots, covariance scores
Return to 2004 working papers list.
Last modified: 2004-10-28 14:02:22 ivo