DNA sequence matching system based on hardware accelerators utilized efficiently in a multithreaded environment

Abstract

Bio Informatics has emerged as one of those sciences in which if knowledge, if exploited ethically, will result in the general benefit of mankind. The enormity of DNA strand data has been revealed to be of humongous proportions. It is imperative to employ the art of parallel and distributed supercomputing in order to process such magnanimous magnitudes of data. We have deployed a scalable array of linearly connected hardware accelerators for the solution of the Smith-Waterman Algorithm; a technique used to resolve sequence alignment of DNA strands. We have synthesized the system on a reconfigurable platform and carried out a performance analysis of the speedup factor accomplished. The system is further connected to a powerful embedded microprocessor which, in a multithreaded environment, serves as an interface to the World Wide Web. This effort is in a bid to bring High-Performance Computing, in this domain, to the doorstep of scientists and enthusiasts alike in a cost-effective manner, thereby, triggering an avalanche of discoveries and providing much needed impetus to scientific work in this area.