QOMA2: Optimizing the alignment of many sequences

Abstract—We consider the problem of aligning multiple protein sequences with the goal of maximizing the SP (Sum-of-Pairs) score, when the number of sequences is large. The QOMA (QuasiOptimal Multiple Alignment) algorithm addressed this problem when the number of sequences is small. However, as the number of sequences increases, QOMA becomes impractical. This paper develops a new algorithm, QOMA2, which optimizes the SP score of the alignment of arbitrarily large number of sequences. Given an initial (potentially sub-optimal) alignment , QOMA2 selects short subsequences from this alignment by placing a window on it. It quickly estimates the amount of improvement that can be obtained by optimizing the alignment of the subsequences in short windows on this alignment. This estimate is called the SW (Sum of Weights) score. It employs a dynamic programming algorithm that selects the set of window positions with the largest total expected improvement. It partitions the subsequences within e...

• Type: Conference
• Year: 2007
• Where: BIBE
• Authors: Xu Zhang, Tamer Kahveci
• Keywords: BIBE 2007, Bioinformatics, Protein Sequences, Sequences, Sp Score