NDLI: Indexing genomic sequences on the IBM Blue Gene

Content Provider	IEEE Xplore Digital Library
Author	Ghoting, A. Makarychev, K.
Copyright Year	2009
Description	Author affiliation: IBM T. J. Watson Res. Center, Yorktown Heights, NY, USA (Ghoting, A.; Makarychev, K.)
Abstract	With advances in sequencing technology and through aggressive sequencing efforts, DNA sequence data sets have been growing at a rapid pace. To gain from these advances, it is important to provide life science researchers with the ability to process and query large sequence data sets. For the past three decades, the suffix tree has served as a fundamental data structure in processing sequential data sets. However, tree construction times on large data sets have been excessive. While parallel suffix tree construction is an obvious solution to reduce execution times, poor locality of reference has limited parallel performance. In this paper, we show that through careful parallel algorithm design, this limitation can be removed, allowing tree construction to scale to massively parallel systems like the IBM Blue Gene. We demonstrate that the entire Human genome can be indexed on 1024 processors in under 15 minutes.
Starting Page	1
Ending Page	11
File Size	385161
Page Count	11
File Format	PDF
ISBN	9781605587448
DOI	10.1145/1654059.1654122
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-11-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Association for Computing Machinery, Inc. (ACM)
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Indexing genomic sequences on the IBM Blue Gene

Indexing genomic sequences on the IBM Blue Gene (2009)

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Indexing genomic sequences on the IBM Blue Gene

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