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The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n3) time using Nussinov’s dynamic programming algorithm. The Four-Russians method is a technique that reduces the running time for certain dynamic programming algorithms by a multiplicative factor after… (More)

Background: The problem of computationally predicting the secondary structure (or folding) of RNA molecules was first introduced more than thirty years ago and yet continues to be an area of active research and development. The basic RNA-folding problem of finding a maximum cardinality, non-crossing, matching of complimentary nucleotides in an RNA sequence… (More)

Several central and well-known combinatorial problems in phylogenetics and population genetics have efficient, elegant solutions when the input is complete or consists of haplotype data, but lack efficient solutions when input is either incomplete, consists of genotype data, or is for problems generalized from decision questions to optimization questions.… (More)

The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known $$O(n^3)$$ O ( n 3 ) -time dynamic programming method. Recently three methodologies—Valiant, Four-Russians, and Sparsification—have been applied to speedup RNA secondary structure prediction. The sparsification method… (More)

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