A Pattern Matching Technique for Multiple Sequences Alignment with GAP Consideration

Abstract

Protein and DNA sequences of different organisms are often related and they indicate the knowledge about species. The consideration is made to align more than two sequences so that a level/extend of similarity or differences be found that would help in categorizing the common characteristics of species and their behaviors. An efficient recursive approach is proposed in this paper that would not only find the multiple sequences Alignment for protein/DNA sequence but also provides means for consideration of gaps between them. The algorithm will calculate the degree of similarity and bounds/extends of gaps to bring refined and useful results. The input variables (e.g. Strands) of the program are user dependant and internal calculations are performed in recursive fashion to add intelligence to the input Strands. Experimental results have shown more favorable performance of the proposed approach as compared to other approaches.