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A Coarse-Grained Reconfigurable Processor for Sequencing and Phylogenetic Algorithms in Bioinformatics
KTH, School of Information and Communication Technology (ICT), Electronic Systems.
KTH, School of Information and Communication Technology (ICT), Electronic Systems.
KTH, School of Information and Communication Technology (ICT), Electronic Systems.ORCID iD: 0000-0003-0565-9376
Department of Computer Science and engineering, Indian Institute of Technology.
2011 (English)In: Proceedings: 2011 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2011, 2011, 190-197 p.Conference paper, Published paper (Refereed)
Abstract [en]

A coarse-grained reconfigurable processor tailoredfor accelerating multiple bioinformatics algorithms isproposed. In this paper, a programmable and scalablearchitectural platform instantiates an array of coarse grainedlight weight processing elements, which allows arbitrarypartitioning, scheduling schemes and capable of solvingcomplete four popular bioinformatics algorithms: theNeedleman-Wunsch, Smith-Waterman, and HMMER onsequencing, and Maximum Likelihood on phylogenetic. Thekey difference of the proposed CGRA based solution comparedto FPGA and GPU based solutions is a much better match onarchitecture and algorithms for the core computational needs,as well as the system level architectural needs. For the samedegree of parallelism, we provide a 5X to 14X speed-upimprovements compared to FPGA solutions and 15X to 78Xcompared to GPU acceleration on 3 sequencing algorithms. Wealso provide 2.8X speed-up compared to FPGA with the sameamount of core logic and 70X compared to GPU with the samesilicon area for Maximum Likelihood.

Place, publisher, year, edition, pages
2011. 190-197 p.
Keyword [en]
Bioinformatics, Coarse Grained Reconfigurable Architecture, Needleman Wunsch, Smith Waterman, HMMER, Maximum Likelihood, Phylogenetic Inference, VLSI
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
URN: urn:nbn:se:kth:diva-73032DOI: 10.1109/ReConFig.2011.1Scopus ID: 2-s2.0-84856915938ISBN: 978-1-4577-1734-5 (print)OAI: oai:DiVA.org:kth-73032DiVA: diva2:488500
Conference
2011 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2011. Cancun, Quintana Roo. 30 November 2011 - 2 December 2011
Note
QC 20120312Available from: 2012-02-01 Created: 2012-02-01 Last updated: 2012-03-12Bibliographically approved

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Hemani, Ahmed

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CiteExportLink to record
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Citation style
  • apa
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