RC-BLAST: towards a portable, cost-effective open source hardware implementation

Basic Local Alignment Search Tool (BLAST) is a standard computer application that molecular biologists use to search for sequence similarity in genomic databases. This paper describes the implementation of an FPGA-based hardware implementation designed to accelerate the BLAST algorithm. FPGA-based custom computing machines, more widely known as reconfigurable computing, are supported by a number of vendors and the basic cost of FPGA hardware is dramatically decreasing. Hence, the main objective of this project is to explore the feasibility of using this new technology to realize a portable, open source FPGA-based accelerator for the BLAST algorithm. The present design is targeted to an AceIIcard and the design is based on the latest version of BLAST available from NCBI. Since the entire application does not fit in hardware, a profile study was conducted that identifies the computationally intensive part of BLAST. An FPGA hardware component has been designed and implemented for this critical segment. The portability and cost-effectiveness of the design are discussed.