FPL Implementation of Systolic Sequence Alignment
Selected papers from the Second International Workshop on Field-Programmable Logic and Applications, Field-Programmable Gate Arrays: Architectures and Tools for Rapid Prototyping
FPL '02 Proceedings of the Reconfigurable Computing Is Going Mainstream, 12th International Conference on Field-Programmable Logic and Applications
Biosequence Similarity Search on the Mercury System
ASAP '04 Proceedings of the Application-Specific Systems, Architectures and Processors, 15th IEEE International Conference
Hyper customized processors for bio-sequence database scanning on FPGAs
Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays
RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Families of FPGA-based accelerators for approximate string matching
Microprocessors & Microsystems
FPGA-accelerated seed generation in Mercury BLASTP
FCCM '07 Proceedings of the 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Design Space Exploration for the BLAST Algorithm Implementation
FCCM '07 Proceedings of the 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
FPGA based architecture for DNA sequence comparison and database search
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
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As one of the most widely used bio-sequence searching tools, BLAST adopts index-based approach to detect the matches between two substrings by looking up a large table and processing one match per query. In this paper, we propose a systolic array approach to detect string matches without using looking up tables. The pipelining systolic array is implemented as a multi-seeds detection and parallel extension pipeline engine to accelerate the first two stages of NCBI BLAST algorithm. Different from the index-based approach, our implementation consumes little memory resources and eliminates redundant string extensions by merging multiple adjoin seeds into a valid seed. Our FPGA implementation achieves superior performance results in both of processing element number and clock frequency over related works in the area of FPGA BLAST accelerators. The experimental results also show the speedup can reach about 17 and 48 compared to the NCBI BLASTp and TBLASTn programs for 3072-residue queries on Intel P4 CPU, respectively. Furthermore, the idea of multi-seeds detection also can be adopted in other seed-based heuristic searching applications.