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Issue No. 03 - July-September (2010 vol. 7)
ISSN: 1545-5963
pp: 495-510
Rezaul Alam Chowdhury , The University of Texas at Austin, Austin
Hai-Son Le , Carnegie Mellon University, Pittsburgh
Vijaya Ramachandran , The University of Texas at Austin, Austin
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.
Sequence alignment, median, RNA secondary structure prediction, dynamic programming, cache-efficient, cache-oblivious.

H. Le, R. A. Chowdhury and V. Ramachandran, "Cache-Oblivious Dynamic Programming for Bioinformatics," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. , pp. 495-510, 2008.
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