Parallel sequence alignment: a lookahead approach

Authors:
Prasanta K. Jana;Nikesh Kumar
Affiliations:
Department of Computer Science and Engineering, Indian School of Mines, Dhanbad, India;Department of Computer Science and Engineering, Indian School of Mines, Dhanbad, India
Venue:
PReMI'05 Proceedings of the First international conference on Pattern Recognition and Machine Intelligence
Year:
2005

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Abstract

In this paper we present a parallel algorithm for local alignment of two biological sequences. Given two sequences of size m and n, our algorithm uses a novel technique namely, carry lookahead and requires O(m / 4 + n / 2) time on a maximum of O(m) processors.