Cache-Oblivious Dynamic Programming for Bioinformatics

— We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alignment and 3-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 cacheoblivious algorithms run faster than software and implementations based on previous best algorithms for these problems.

• Type: Journal
• Year: 2010
• Where: TCBB
• Authors: Rezaul Alam Chowdhury, Hai-son Le, Vijaya Ramachandran
• Keywords: Algorithms, Cache-oblivious Algorithms, Sequence Alignment, TCBB 2010