Cache-Oblivious Dynamic Programming for Bioinformatics

Rezaul Alan Chowdhury, Hai-Son Le, Vijaya Ramachandran
2010 IEEE/ACM Transactions on Computational Biology & 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
more » ... ver 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. Index Terms-sequence alignment, median, RNA secondary structure prediction, dynamic programming, cache-efficient, cache-oblivious.
doi:10.1109/tcbb.2008.94 pmid:20671320 fatcat:vn2vc4qlqnervbqj3veiyt36e4