Space-efficient Parallel Algorithms for the Constrained Multiple Sequence Alignment Problem

Given sequences S1, S2, . . . Sn, and a pattern stringP the constrained multiple sequence alignment problem (CMSA) is to align similar subsequences of these sequences with the constraint that the alignment “contains” P . TheCMSA problem can be considered as an optimal path search problem in the dynamic programming matrix. The problem has a dynamic programming solution that requiresO(2|S1||S2|...|Sn||P |) time and O(|S1||S2|...|Sn||P |) space where |S1|, |S2|, ..., |Sn| are the lengths of sequences S1, S2, ..., Sn, and |P | is the length of the pattern string, respectively. There is a parallel algorithm that uses|P | + 1 processors. The algorithm requiresO(|S1||S2|...|Sn|) space for each processor. The memory requirement is a major bottleneck for theCMSA problem. In this paper, we propose two parallel algorithms which solve the CMSA problem and use less space on each processor than the ordinary dynamic programming algorithm and existing parallel algorithms for the problem.

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