Cache-Oblivious Dynamic Programming for Bioinformatics

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 7; no. 3; pp. 495 - 510
• Main Authors: Chowdhury, Rezaul Alan, Hai-Son Le, Ramachandran, Vijaya
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.07.2010; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithm design and analysis; Algorithms; Base Pairing; Base Sequence; Bioinformatics; Biology computing; cache-efficient; cache-oblivious; Computational Biology - methods; Costs; Dynamic programming; Heuristic algorithms; median; Nucleic Acid Conformation; Partitioning algorithms; Polynomials; RNA; RNA - chemistry; RNA secondary structure prediction; Sequence alignment; Sequence Alignment - methods; Software; Software algorithms; Combinatorial algorithms; Theory of Computation; Biology and genetics; Tradeoffs between Complexity Measures; Analysis of Algorithms and Problem Complexity
• ISSN: 1545-5963; 1557-9964; 1557-9964
• DOI: 10.1109/TCBB.2008.94

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.