NDLI: MEMOCODE 2012 hardware/software codesign contest: DNA sequence aligner

Content Provider	IEEE Xplore Digital Library
Author	Edwards, S.A.
Copyright Year	2012
Description	Author affiliation: Department of Computer Science, Columbia University, New York, NY, USA (Edwards, S.A.)
Abstract	The MEMOCODE design contest for 2012 is exact substring matching: a simplified form of the DNA sequence alignment problem. The challenge is to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome. Contestants had a month to create a fast system that ran on a given set of test data. Entries were judged both on absolute time and the product of time and system cost. The two winning groups, which were invited to contribute papers describing their solutions, judiciously chose algorithms that exploited powerful hardware. The two winning entries employed a hash algorithm running on a Convey HC-1 FPGA/multicore hybrid with an aggressive memory system and a Burrows-Wheeler/hash hybrid running on a 12-core Intel system was second.
Starting Page	85
Ending Page	90
File Size	199208
Page Count	6
File Format	PDF
ISBN	9781467313148
e-ISBN	9781467313131
DOI	10.1109/MEMCOD.2012.6292303
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-07-16
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genomics Bioinformatics DNA Educational institutions Humans Runtime Indexes FPGAs DNA sequence alignment string matching hardware/software codesign GPGPUs Multicore
Content Type	Text
Resource Type	Article

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