Prediction and alignment of RNA pseudoknot structures are NP-hard. Nevertheless, several efficient prediction algorithms by dynamic programming have been proposed for restricted cl...
We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the MAXIMUM BASE PAIR STACKINGS problem proposed by Ieon...
Seq7 is a newprogramfor generating multiple structure-based alignments of RNAsequences. Byusing a variant of Dijkstra’s algorithm to find the shortest path through a specially c...