Cache-Oblivious Dynamic Programming for Bioinformatics
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.
- Publication:
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IEEE Transactions on Computational Biology and Bioinformatics
- Pub Date:
- 2010
- DOI:
- Bibcode:
- 2010ITCBB...7..495C
- Keywords:
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- Sequence alignment;
- median;
- RNA secondary structure prediction;
- dynamic programming;
- cache-efficient;
- cache-oblivious