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Improved Bioinformatics Processing Unit for Multiple Applications
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
2012 (English)In: Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2012, IEEE , 2012, 390-396 p.Conference paper, Published paper (Refereed)
Abstract [en]

This paper presents a coarse-grain reconfigurable unit for accelerating multiple widely used bioinformatics algorithms. Our design is a highly efficient, programmable bioinformatics processing unit, called BiCell v2. Based on a specialized multimode multiplier, this unit provides three different working modes, in order to accelerate four popular bioinformatics algorithms: Maximum Likelihood based phylogenetic inference, Needleman-Wunsch, Smith-Waterman, and HMMER in sequence alignment. BiCell v2 supports both single and double precision floating-point computation, which significantly increases the accuracy for bioinformatics algorithm acceleration but retains silicon area efficiency. Making use of this improved processing unit, our platform gives about 10X speedup compared to our previous design in single-precision, and 23.2X speedup comparing with GPGPU in the same precision.

Place, publisher, year, edition, pages
IEEE , 2012. 390-396 p.
Series
IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum-IPDPSW, ISSN 2164-7062
Keyword [en]
component, Bioinformatics, Coarse-Grained, Reconfigurable Architecture, Phylogenetic Inference, Needleman-Wunsch, Smith- Waterman, HMMER, Maximum-Likelihood, VLSI
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
URN: urn:nbn:se:kth:diva-105620DOI: 10.1109/IPDPSW.2012.48ISI: 000309409400045Scopus ID: 2-s2.0-84867436208ISBN: 978-0-7695-4676-6 (print)OAI: oai:DiVA.org:kth-105620DiVA: diva2:571541
Conference
2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2012; Shanghai; 21 May 2012 through 25 May 2012
Note

QC 20121123

Available from: 2012-11-23 Created: 2012-11-23 Last updated: 2012-11-23Bibliographically approved

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Hemani, Ahmed

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