Parallel Lcs Algorithm for Pairwise Sequence Alignment
Abstract
Multicore processors are gaining ground in the world of modern computers. With faster performance, it would allow DNA or protein alignment, which is a fundamental procedure in molecular biology, to be done faster, paving the way to faster multiple genome comparison. However, in order to harvest the advantages of multicore processors, corresponding parallel algorithms need to be developed and tested. This study aimed to develop a suitable parallel longest common subsequence (LCS) algorithm for pairwise alignment. The proposed parallel LCS performed approximately 30-40% faster than serial LCS, while yielding the same alignment results. Index Terms—Parallel algorithm; longest common subsequence; biological sequence alignment; computational biology
Authors: Pich Tantichukaitikul, Sattara Hattirat, Jonathan H. Chan