Parallel computing for optimal genomic sequence alignment

Authors:
Zhihua Du;Zhen ji;Feng Lin
Affiliations:
Faculty of Information Engineering, Shenzhen University, Shenzhen, China;Faculty of Information Engineering, Shenzhen University, Shenzhen, China;School of computer engineering, Nanyang Technological University, Singapore
Venue:
FSKD'06 Proceedings of the Third international conference on Fuzzy Systems and Knowledge Discovery
Year:
2006

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Abstract

This paper presents a new parallel algorithm, called “block-based wavefront”, to produce optimal pairwise alignment for biological sequences with reliable output and reasonable cost. It takes advantage of dynamic programming and parallel computing to produce optimal results in reasonable time. More importantly, the algorithm makes it possible for biologists to analyze datasets that were previously considered too long, often leading to memory overflow or prohibitively long time for computation.