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    BMCBI
    2007
    233views more  BMCBI 2007»
    160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
    13 years 5 months ago
    160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
    Download  www.biomedcentral.com
    Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
    Isaac T. S. Li, Warren Shum, Kevin Truong
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    ISPDC
    2007
    IEEE
    87views Distributed And Parallel Com...» more  ISPDC 2007»
    Whole Genome Comparison on a Network of Workstations
    13 years 11 months ago
    Whole Genome Comparison on a Network of Workstations
    Download  www.tifr.res.in
    Whole genome comparison consists of comparing or aligning genome sequences with a goal of finding similarities between them. Previously we have shown how SIMD Extensions used in ...
    Arpith C. Jacob, Sugata Sanyal, Marcin Paprzycki, ...
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    BIBE
    2008
    IEEE
    142views Bioinformatics» more  BIBE 2008»
    Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
    13 years 11 months ago
    Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
    Download  people.cs.vt.edu
    — The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
    Ashwin M. Aji, Wu-chun Feng
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    PROCEDIA
    2010
    138views more  PROCEDIA 2010»
    Using the reconfigurable massively parallel architecture COPACOBANA 5000 for applications in bioinformatics
    12 years 11 months ago
    Using the reconfigurable massively parallel architecture COPACOBANA 5000 for applications in bioinformatics
    Download  www.informatik.uni-kiel.de
    Currently several computational problems require high processing power to handle huge amounts of data, although underlying core algorithms appear to be rather simple. Especially i...
    Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Car...
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    IPPS
    2006
    IEEE
    139views Distributed And Parallel Com...» more  IPPS 2006»
    Bio-sequence database scanning on a GPU
    13 years 11 months ago
    Bio-sequence database scanning on a GPU
    Download  www.hicomb.org
    Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic programming algorithms exist for t...
    Weiguo Liu, Bertil Schmidt, Gerrit Voss, Adrian Sc...
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