The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
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Multiple sequence alignment (MSA) is one of the most basic and central tasks for many studies in modern biology. In this paper, we present a new progressive alignment algorithm for this very difficult problem. Given two groups A and B of aligned sequences, this algorithm uses Dynamic Programming and the sum-of-pairs objective function to determine an optimal alignment C of A and B. The proposed algorithm has a much lower time complexity compared with a previously published algorithm for the same task [11]. Its performance is extensively assessed on the well-known BAliBase benchmarks and compared with several state-of-the-art MSA tools.