A general reconfigurable architecture for the BLAST algorithm

The process of DNA sequence matching and database search is one of the major problems of the bioinformatics community. Major scientific efforts to address this problem have provided algorithms and software tools for molecular biologists since the early 1970s. At the algorithmic and software level BLAST is by far the most popular tool. It has been developed and continues to be maintained and distributed by the NCBI organization. The BLAST algorithm and software is computationally very intensive and as a result several computer vendors use it as a benchmark. On the other hand no systematic approach for hardware speedup of BLAST and its variants for different query and database size has been reported to date. In this paper we present our architecture that implements the BLAST algorithm for all of its major versions, and for any size of database and query. The system has been fully designed and partially implemented with reconfigurable logic. It consists of software and hardware parts and achieves a speedup of several times up to thousands of times vs general purpose computers.