A General Reconfigurable Architecture for the BLAST Algorithm
Journal of VLSI Signal Processing Systems
A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms
Journal of VLSI Signal Processing Systems
Single pass streaming BLAST on FPGAs
Parallel Computing
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Scalable multigigabit pattern matching for packet inspection
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
DNA Physical Mapping on a Reconfigurable Platform
ARC '08 Proceedings of the 4th international workshop on Reconfigurable Computing: Architectures, Tools and Applications
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
Finding the Next Computational Model: Experience with the UCSC Kestrel
Journal of Signal Processing Systems
Acceleration of ungapped extension in Mercury BLAST
Microprocessors & Microsystems
Fast and accurate NCBI BLASTP: acceleration with multiphase FPGA-based prefiltering
Proceedings of the 24th ACM International Conference on Supercomputing
INES'10 Proceedings of the 14th international conference on Intelligent engineering systems
Vision for liquid architecture
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Auto-pipe and the X language: a pipeline design tool and description language
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
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Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume,high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described.