PARALELL IMPLEMENTATION OF THE SIMILARITY MATRIX USING THREADS

Sequence comparison is one of the key concepts in determining the functional properties of proteins. Determining the similarity between a given gene and genes in a database tells much about the behavior of that gene. The classical algorithm for computing the similarity between two sequences uses the dynamic programming matrix and compares the two strings with time complexity O(n2). This paper addresses the challenge of computing the similarity between two DNA molecules with a time complexity less than O(n2) by using multithreaded approach. The algorithm requires the use of a multiprocessor machine to enhance the use of threads. The algorithm divides the similarity matrix into blocks, each of which represents a column. A thread is assigned to each block, and all collaborate to build the similarity matrix. The work is divided between threads to find optimal solution