Performance evaluation of BLAST on SMP machines

BLAST is a tool for finding biologically similar sequences to given query sequences in annotated sequence database. Since the number of sequences in the database increases at exponential rate, and the number of users drastically increases, the performance of BLAST is a primary concern to service sites like NCBI. NCBI developed a parallel BLAST for the speedup of BLAST using threads on SNIP machines. But the speedup is still limited due to the architectural limitations of SNIP machines. Distributed memory multiprocessor can be an alternative choice for cost-effective search in very large scale sequence data. However for an optimized configuration of Cluster systems and SMP machines, the performance study of BLAST on SNIP machines is essential. In this paper, we analyze BLAST and BLAST algorithms to enhance the performance of BLAST on parallel machines and report the performance of BLAST on SMP machines. Some important runtime characteristics of BLAST are identified through the performance evaluation. According to our performance test, PC clusters or clusters of low-way SNIP machines outperform high-way SNIP machines in terms of cost-effectiveness. Besides, BLAST on Linux operating system shows better performance than BLAST on Solaris operating system in the same configurations.