Efficient parallel algorithms for processing biological sequences
by S. Rajasekaran, R. Ammar, D.G. Shin, G. Zhang
International Journal of Computer Applications in Technology (IJCAT), Vol. 26, No. 3, 2006

Abstract: Processing of biological sequences is a compute-intensive problem. The amount of data available in biology is so enormous that sequential techniques take a very long time to process them. In this paper, we present some parallel algorithms for biological data processing. We consider a scenario where the operations performed on the sequences are arbitrary. In particular, we assume that a sequential algorithm can be executed in parallel by a number of processors on an input consisting of a file of sequences to be processed. The goal is to process all these sequences as efficiently as possible. We present four parallel algorithms in this paper: Algorithms 1-4. Algorithm 1 is shown to be (1+α)-competitive with high probability for any fixed α>0 under suitable assumptions. Algorithm 2 is shown to be O(1)-competitive and Algorithm 3 is shown to be 2-competitive. We have experimentally compared the performance of these four algorithms and the results are presented.

Online publication date: Mon, 07-Aug-2006

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