DNA fingerprint using smith waterman algorithm by grid computing

Abstract

Deoxyribonucleic acid (DNA) is a molecule that encodes unique genetic instructions used in the development and functioning of all known living organisms and many viruses. This Genetic information is encoded as a sequence of nucleotides (adenine, cytosine, guanine, and thymine) recorded using the letters A, C, G, and T. DNA querying or alignment of these sequences required dynamic programming tools and very complex matrices and some heuristic methods like fast-all protein or nucleotide (FASTA) and Basic Local Alignment Search Tool (BLAST) that use massive force of processing and highly time consuming. We present a parallel solution to reduce the processing time. Smith waterman algorithm, some weighting matrices and a grid of computers are used to And field of similarity between these sequences in large DNA datasets. This grid consists of master computer and unlimited number of agents. The master computer is the user interface for insert the queried sequence and coordinates the processing between the grid agents.