[show abstract][hide abstract] ABSTRACT: Predicting the secondary structure of an RNA sequence is an important problem in structural bioinformatics. The general RNA folding problem, where the sequence to be folded may contain pseudoknots, is computationally intractable when no prior knowledge on the pseudoknot structures the sequence contains is available. In this paper, we consider stable stems in an RNA sequence and provide a new characterization for its stem graph, a graph theoretic model that has been used to describe the overlapping relationships for stable stems. Based on this characterization, we identify a new,structure parameter for a stem graph. We call this structure parameter crossing width. We show that given a sequence with crossing width c for its stem graph, the general RNA folding problem can be solved in timeO(2, when,the maximum,stem length is bounded,by a constant. Keywords: RNA secondary structure prediction, pseudoknot, free en-
Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings; 01/2007
[show abstract][hide abstract] ABSTRACT: A new bijection between 3-Motzkin paths and Schröder paths with no peak at odd height is presented, together with numerous consequences involving related combina-torial structures such as 2-Motzkin paths, ordinary Motzkin paths and Dyck paths.