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 alternate method to obtain global alignment between two sequences using logic gates and compare the performance of our algorithm with that of the classical method.

Key words: DNAsequencing –Sequence alignment –Binary representation – Logic gates – Graph Coincidence.