Tree adjoining grammars for RNA structure prediction
Theoretical Computer Science - Special issue: Genome informatics
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Dynamic Programming on Graphs with Bounded Treewidth
ICALP '88 Proceedings of the 15th International Colloquium on Automata, Languages and Programming
Rapid ab initio RNA folding including pseudoknots via graph tree decomposition
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Impact of the energy model on the complexity of RNA folding with pseudoknots
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
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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 time O(2ck3n2), where n is the length of the sequence, k is the maximum length of stable stems. Moreover, this characterization leads to an O(2(1+2k2)nn2k3) time algorithm for the general RNA folding problem where the lengths of stems in the sequence are at most k, this result improves the upper bound of the problem to 2O(n)n2 when the maximum stem length is bounded by a constant.