Parallel processing of biological sequence comparison algorithms
International Journal of Parallel Programming
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
Space and Time Optimal Parallel Sequence Alignments
IEEE Transactions on Parallel and Distributed Systems
Scalable hardware accelerator for comparing DNA and protein sequences
InfoScale '06 Proceedings of the 1st international conference on Scalable information systems
Families of FPGA-based accelerators for approximate string matching
Microprocessors & Microsystems
A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
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Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Knownmethods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.