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Hi-per BLAST: High Performance BLAST on PC Cluster System

BLAST [1] is a homology search tool to identify new DNA/protein sequences. It is considered as the fastest among several homology search tools, and improved and maintained by several organizations. Above all, NCBI BLAST [3] developed by NCBI is accepted as a defacto standard and widely used. NCBI BLAST is fast, however, it is getting longer to complete a BLAST run. That is mainly because the size of database grows rapidly. As a matter of fact, the size of DNA database becomes twice a year recently [2]. The pace of database growth exceeds that of performance growth of a single CPU. Therefore, a parallel version of BLAST that can effectively use multiple CPUs is desired. Several organizations such as TurboWorx Inc. [5] and Paracel Inc. [4] are developing the parallel version of BLAST. Our Hi-per BLAST is such a parallel version of BLAST, based on NCBI BLAST. The performance of Hi-per BLAST shows almost linear speedup to the number of CPUs, and over linear speedup in some cases. In this paper, we first explain the components and the execution process of Hi-per BLAST, then show the performance measurement results on a Fujitsu PRIMERGY server cluster system.