DNA Sequence Matching Using Boolean Algebra

Alignment is the most basic component of biological sequence manipulation and has diverse applications in sequence assembly, sequence annotation, structural and functional predictions for genes and proteins, phylogeny and evolutionary analysis. Classical methods like Needleman Wunsch ( for global alignment) in 1970 and Smith-Waterman (for local alignment) in 1981 suffer from the drawback that it involves a large number of computational steps and has a statically allocate a large section of memory for computer implementation. This paper suggests an algorithm for global alignment between two DNA sequences and compares the performance of the algorithm with Needleman Wunsch. Complexity calculation shows that the proposed algorithm has a much less time complexity and requires very much less amount of memory storage than Needleman Wunsch algorithm.