The Performance of Sequence Alignment Algorithms

Abstract: This thesis deals with sequence alignment algorithms. The sequence alignment is a mutual arrange of two or more sequences in order to study their similarity and dissimilarity. Four decades after the seminal work by Needleman and Wunsch in 1970, these methods still need more explorations. We start out with a review of a sequence alignment, and its generalization to multiple alignments, although the focus of this thesis is on the evaluation of the new alignment algorithms. The research presented here in has stepped into the different algorithms that are in terms of the dynamic programming. In the study of sequence alignment algorithms, two powerful techniques have been invented. According to the simulations, the new algorithms are shown to be extremely efficient for the comparing DNA sequences. All the sequence alignment algorithmsare compared in terms of the distance. We use the programming language R for the implementation and simulation of the algorithms discussed in this thesis.