Theoretical Computer Science
Efficient Hardware Hashing Functions for High Performance Computers
IEEE Transactions on Computers
Communications of the ACM
Perfect hashing functions: a single probe retrieving method for static sets
Communications of the ACM
Space/time trade-offs in hash coding with allowable errors
Communications of the ACM
Journal of Algorithms
Kestrel: A Programmable Array for Sequence Analysis
ASAP '96 Proceedings of the IEEE International Conference on Application-Specific Systems, Architectures, and Processors
A New Hardware Architecture for Genomic and Proteomic Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
An Architecture for Fast Processing of Large Unstructured Data Sets
ICCD '04 Proceedings of the IEEE International Conference on Computer Design
Merrimac: Supercomputing with Streams
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Designing seeds for similarity search in genomic DNA
Journal of Computer and System Sciences - Special issue on bioinformatics II
The Mercury system: exploiting truly fast hardware for data search
SNAPI '03 Proceedings of the international workshop on Storage network architecture and parallel I/Os
Language classification using n-grams accelerated by FPGA-based Bloom filters
HPRCTA '07 Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications: held in conjunction with SC07
Visions for application development on hybrid computing systems
Parallel Computing
Mercury BLASTP: Accelerating Protein Sequence Alignment
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
A Reconfigurable Bloom Filter Architecture for BLASTN
ARCS '09 Proceedings of the 22nd International Conference on Architecture of Computing Systems
Application-guided tool development for architecturally diverse computation
Proceedings of the 2010 ACM Symposium on Applied Computing
Reconfigurable accelerator for the word-matching stage of BLASTN
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
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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.