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» Multiple Sequence Alignment Using Reconfigurable Computing
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BIOCOMP
2006
14 years 11 months ago
Performance of Sequence Alignment Bioinformatics Applications on General Purpose Processors: A Case Study
- Aligning specific sequences against other known sequences in a database is a central aspect of bioinformatics. New experimental data being added continuously to these databases n...
Pradeep Nair, Eugene John
ICPP
2003
IEEE
15 years 2 months ago
FastLSA: A Fast, Linear-Space, Parallel and Sequential Algorithm for Sequence Alignment
Pairwise sequence alignment is a fundamental operation for homology search in bioinformatics. For two DNA or protein sequences of length ¢ and £ , full-matrix (FM), dynamic prog...
Adrian Driga, Paul Lu, Jonathan Schaeffer, Duane S...
CSB
2003
IEEE
128views Bioinformatics» more  CSB 2003»
15 years 3 months ago
Degenerate Primer Design via Clustering
This paper describes a new strategy for designing degenerate primers for a given multiple alignment of amino acid sequences. Degenerate primers are useful for amplifying homologou...
Xintao Wei, David N. Kuhn, Giri Narasimhan
IPPS
2003
IEEE
15 years 2 months ago
Sequence Alignment on the Cray MTA-2
The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigatio...
Shahid H. Bokhari, Jon R. Sauer
ERSA
2004
134views Hardware» more  ERSA 2004»
14 years 11 months ago
A High Performance Application Representation for Reconfigurable Systems
Modern reconfigurable computing systems feature powerful hybrid architectures with multiple microprocessor cores, large reconfigurable logic arrays and distributed memory hierarch...
Wenrui Gong, Gang Wang, Ryan Kastner