Cache-Oblivious Dynamic Programming for Bioinformatics

Authors:
Rezaul Alan Chowdhury;Hai-Son Le;Vijaya Ramachandran
Affiliations:
The University of Texas at Austin, Austin;Carnegie Mellon University, Pittsburgh;The University of Texas at Austin, Austin
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2010

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Abstract

We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alignment and three-way sequence alignment (or median), both with affine gap costs, and RNA secondary structure prediction with simple pseudoknots. For each of these problems, we present cache-oblivious algorithms that match the best-known time complexity, match or improve the best-known space complexity, and improve significantly over the cache-efficiency of earlier algorithms. We present experimental results which show that our cache-oblivious algorithms run faster than software and implementations based on previous best algorithms for these problems.