Kestrel: A Programmable Array for Sequence Analysis
ASAP '96 Proceedings of the IEEE International Conference on Application-Specific Systems, Architectures, and Processors
Biosequence Similarity Search on the Mercury System
ASAP '04 Proceedings of the Application-Specific Systems, Architectures and Processors, 15th IEEE International Conference
Efficient Data Access for Parallel BLAST
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01
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
The Mercury system: exploiting truly fast hardware for data search
SNAPI '03 Proceedings of the international workshop on Storage network architecture and parallel I/Os
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Biosequence Similarity Search on the Mercury System
Journal of VLSI Signal Processing Systems
Single pass streaming BLAST on FPGAs
Parallel Computing
Some initial results on hardware BLAST acceleration with a reconfigurable architecture
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Accelerating BLASTP on the Cell Broadband Engine
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
High performance protein sequence database scanning on the Cell Broadband Engine
Scientific Programming - High Performance Computing with the Cell Broadband Engine
Application-guided tool development for architecturally diverse computation
Proceedings of the 2010 ACM Symposium on Applied Computing
Fast and accurate NCBI BLASTP: acceleration with multiphase FPGA-based prefiltering
Proceedings of the 24th ACM International Conference on Supercomputing
Deadlock avoidance for streaming computations with filtering
Proceedings of the twenty-second annual ACM symposium on Parallelism in algorithms and architectures
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this article, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11--15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results.