Space and Time Optimal Parallel Sequence Alignments

• Authors: Stjepan Rajko;Srinivas Aluru
• Venue: IEEE Transactions on Parallel and Distributed Systems
• Year: 2004

We present the first space and time optimal parallel algorithm for the pairwise sequence alignment problem, a fundamental problem in computational biology. This problem can be solved sequentially inO(mn) time andO(m+n) space, wherem andn are the lengths of the sequences to be aligned. The fastest known parallel space-optimal algorithm for pairwise sequence alignment takes optimalO\left({{m+n}\over{p}}\right) space, but suboptimalO\left({{(m+n)^2}\over{p}}\right) time, wherep is the number of processors. On the other hand, the most space economical time-optimal parallel algorithm takesO\left({{mn}\over{p}}\right) time, butO\left(m+{{n}\over{p}}\right) space. We close this gap by presenting an algorithm that achieves both time and space optimality, i.e. requires onlyO\left({{m+n}\over{p}}\right) space andO\left({{mn}\over{p}}\right) time. We also present an experimental evaluation of the proposed algorithm on an IBM xSeries cluster. Although presented in the context of full sequence alignments, our algorithm is applicable to other alignment problems in computational biology including local alignments and syntenic alignments. It is also a useful addition to the range of techniques available for parallel dynamic programming.