Parallel Three-sequence Alignment with Space-efficient

The sequence alignment is a fundamental problem in computational biology. Many sequence alignment methods have been proposed, such as pair-wise sequence alignment, multiple sequence alignment (MSA), syntenic alignment, constraint multiple sequence alignment, and etc. Among them, pair-wise sequence alignment is a most commonly used method. Recently, MSA is more and more important which has been used to solve many molecular biological problems. The sum-of-pairs MSA problem has been proved to be a NP-complete problem. A progressive algorithm was used to solve MSA problem which is based on the pair-wise sequence alignments. However, this progressive MSA has a problem. This problem may be solved by using three-sequence alignment as a basic step instead of pair-wise sequence alignment. Three-sequence alignment can be solved sequentially in O(mnl) time complexity and O(mn) space complexity, where m, n and l are the lengths of the sequences to be aligned. The complexities of three-sequence alignment limit its applicability. Hence, to reduce the complexities becomes an important issue. In this paper, we propose a parallel algorithm to solve this problem. Our parallel algorithm requires O((mn)/p) space complexity and O((mnl)/p) time complexity, where p is the number of processors. Both experimental results and theoretical analysis are presented. The experimental results show that our parallel algorithm is applicable and achieves a good speed up.