A New Hardware Architecture for Genomic and Proteomic Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics 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
A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
Families of FPGA-based accelerators for approximate string matching
Microprocessors & Microsystems
A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
Single pass streaming BLAST on FPGAs
Parallel Computing
Processor array architectures for flexible approximate string matching
Journal of Systems Architecture: the EUROMICRO Journal
Hardware BLAST Algorithms with Multi-seeds Detection and Parallel Extension
ARC '08 Proceedings of the 4th international workshop on Reconfigurable Computing: Architectures, Tools and Applications
Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Multiple Sequence Alignment Based on Dynamic Programming Using FPGA
IEICE - Transactions on Information and Systems
FPGA supercomputing solution for Peptide Mass Fingerprinting
BioMED '08 Proceedings of the Sixth IASTED International Conference on Biomedical Engineering
Exhaustive peptide searching using relations
BNCOD'07 Proceedings of the 24th British national conference on Databases
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
Hardware designs for local alignment of protein sequences
ISCIS'06 Proceedings of the 21st international conference on Computer and Information Sciences
Multidimensional dynamic programming for homology search on distributed systems
Euro-Par'06 Proceedings of the 12th international conference on Parallel Processing
Microprocessors & Microsystems
Optimization schemes and performance evaluation of Smith–Waterman algorithm on CPU, GPU and FPGA
Concurrency and Computation: Practice & Experience
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As the emerging field of bioinformatics continues to expand, the ability to rapidly search large databases of genetic information is becoming increasingly important. Databases containing billions of data elements are routinely compared and searched for matching and near-matching patterns. In this paper we explore the use of run-time reconfiguration using field programmable gate arrays (FPGAs) to provide a compact, high-performance matching solution to accelerate the searching of these genetic databases. This implementation provides approximately an order of magnitude increase in performance while reducing hardware complexity by as much as three orders of magnitude when compared to existing commercial systems.