Using blocks+ database in Needleman-Wunsch algorithm

This paper describes a novel approach of computing pairwise sequence alignment for guarantee that the generated alignment satisfies some particular blocks that should be aligned together. This approach can increase the accuracy of the resulting alignment by incorporating prior knowledge about the sequences. It brings into the alignment the method used by biologists which consists of forcing the alignment of occurrences in certain biological structures or functions. In the first part, the problem of this algorithm is outlined. Later, a general introduction of related work is described. Finally, a modified Needleman-Wunsch algorithm and experimental results are presented. The importance of this process lies on its effect of keeping common blocks in sequences to be aligned accurately.