Journal of VLSI Signal Processing Systems
A programmable array processor architecture for flexible approximate string matching algorithms
Journal of Parallel and Distributed Computing
Biosequence Similarity Search on the Mercury System
Journal of VLSI Signal Processing Systems
Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform
HPRCTA '07 Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications: held in conjunction with SC07
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Finding the Next Computational Model: Experience with the UCSC Kestrel
Journal of Signal Processing Systems
Acceleration of ungapped extension in Mercury BLAST
Microprocessors & Microsystems
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Kestrel is a programmable linear systolic array processor designed for sequence analysis. Among other features, Kestrel includes an 8-bit word, a single-cycle add-and-minimize instruction, and efficient communication using Systolic Shared Registers. This paper describes Kestrel's functional units in detail, and examines each of their effects on system performance. With prototypes currently in the works, we expect to complete a full Kestrel array, with between 512 and 1024 processing elements, in 1997.