A New Dynamic Programming Algorithm for Multiple Sequence Alignment

Abstract. 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.

• Type: Conference
• Year: 2007
• Where: COCOA
• Authors: Jean-Michel Richer, Vincent Derrien, Jin-Kao Hao
• Keywords: COCOA 2007, Multiple Sequence Alignment, Progressive Alignment Algorithm, State-of-the-art Msa Tools