BLAST
Biosequence Similarity Search on the Mercury System
ASAP '04 Proceedings of the Application-Specific Systems, Architectures and Processors, 15th IEEE International Conference
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
Single pass streaming BLAST on FPGAs
Parallel Computing
Compressed indexing and local alignment of DNA
Bioinformatics
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Reconfigurable Computing: The Theory and Practice of FPGA-Based Computation
Reconfigurable Computing: The Theory and Practice of FPGA-Based Computation
CAAD BLASTP: NCBI BLASTP Accelerated with FPGA-Based Accelerated Pre-Filtering
FCCM '09 Proceedings of the 2009 17th IEEE Symposium on Field Programmable Custom Computing Machines
Improvement of BLASTp on the FPGA-Based high-performance computer RIVYERA
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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NCBI BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. The problem is that it uses complex heuristics which make it difficult to simultaneously achieve both substantial speed-up and exact agreement with the original output. We have previously described how a novel FPGA-based prefilter that performs exhaustive ungapped alignment (EUA) could be used to reduce the computation by over 99.9% without loss of sensitivity. The primary contribution here is to show how the EUA filter can be combined with another filter, this one based on standard 2-hit seeding. The result is a doubling of performance over the previous best implementation, which itself is an order of magnitude faster than the unaccelerated original. Other contributions include new algorithms for both the original EUA and the 2-hit filters and experimental results demonstrating their utility. This new multiphase FPGA-accelerated NCBI BLASTP scales easily and is appropriate for use in large FPGA-based servers such as the Novo-G.