SPAA '92 Proceedings of the fourth annual ACM symposium on Parallel algorithms and architectures
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
Implementing an API for Distributed Adaptive Computing Systems
FCCM '99 Proceedings of the Seventh Annual IEEE Symposium on Field-Programmable Custom Computing Machines
A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
Examining the viability of FPGA supercomputing
EURASIP Journal on Embedded Systems
A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
Processor array architectures for flexible approximate string matching
Journal of Systems Architecture: the EUROMICRO Journal
Multiple Sequence Alignment Based on Dynamic Programming Using FPGA
IEICE - Transactions on Information and Systems
Impact of high-level transformations within the ROCCC framework
ACM Transactions on Architecture and Code Optimization (TACO)
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
A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
Dynamic data folding with parameterizable FPGA configurations
ACM Transactions on Design Automation of Electronic Systems (TODAES)
Multidimensional dynamic programming for homology search on distributed systems
Euro-Par'06 Proceedings of the 12th international conference on Parallel Processing
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Advances in the field of bio-technology has led to anever increasing demand for computational resourcesto rapidly search large databases of genetic information.Databases with billions of data elements are routinelycompared and searched for matching and near-matchingpatterns. In this paper we present a systemdeveloped to search DNA sequence data using runtimereconfiguration of Field Programmable Gate Arrays(FPGAs). The system provides an order of magnitudeincrease in performance while reducing hardwarecomplexity when compared to existing commercial systems.