The Design, Implementation, and Evaluation of mpiBLAST

Abstract

mpiBLAST is an open-source parallelization of BLAST that achieves superlinear speed-up by segmenting a BLAST database and then having each node in a computational cluster search a unique portion of the database. Database segmentation permits each node to search a smaller portion of the database, eliminating disk I/O and vastly improving BLAST performance. Because database segmentation does not create heavy communication demands, BLAST users can take advantage of low-cost and efficient Linux cluster architectures such as the bladed Beowulf. In addition to presenting the software architecture of mpiBLAST we present a detailed performance analysis of mpiBLAST to demonstrate its scalability.