Reconfigurable computing: a survey of systems and software
ACM Computing Surveys (CSUR)
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
A Run-Time Reconfigurable System for Gene-Sequence Searching
VLSID '03 Proceedings of the 16th International Conference on VLSI Design
Biosequence Similarity Search on the Mercury System
ASAP '04 Proceedings of the Application-Specific Systems, Architectures and Processors, 15th IEEE International Conference
Rapid Phototyping of a System-on-a-Chip for the BLAST Algorithm Implementation
RSP '06 Proceedings of the Seventeenth IEEE International Workshop on Rapid System Prototyping
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Some initial results on hardware BLAST acceleration with a reconfigurable architecture
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
FPGA based architecture for DNA sequence comparison and database search
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Fast and accurate NCBI BLASTP: acceleration with multiphase FPGA-based prefiltering
Proceedings of the 24th ACM International Conference on Supercomputing
Design and implementation of a database filter for BLAST acceleration
Proceedings of the Conference on Design, Automation and Test in Europe
A special-purpose architecture for solving the breakpoint median problem
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
Exploring online synthesis for CGRAs with specialized operator sets
International Journal of Reconfigurable Computing - Special issue on selected papers from the international workshop on reconfigurable communication-centric systems on chips (ReCoSoC' 2010)
Towards automatic detecting of overlapping genes - clustered BLAST analysis of viral genomes
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Towards systolic hardware acceleration for local complexity analysis of massive genomic data
Proceedings of the great lakes symposium on VLSI
Improvement of BLASTp on the FPGA-Based high-performance computer RIVYERA
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
FPGA-based hardware acceleration for local complexity analysis of massive genomic data
Integration, the VLSI Journal
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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.