NDLI: Hyper customized processors for bio-sequence database scanning on FPGAs

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Hyper customized processors for bio-sequence database scanning on FPGAs

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Hyper customized processors for bio-sequence database scanning on FPGAs

Content Provider	ACM Digital Library
Author	Oliver, Tim Maskell, Douglas Schmidt, Bertil
Abstract	Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic-programming algorithms exist for solving this problem, however current solutions still require significant scan times. These scan time requirements are likely to become even more severe due to exponential database growth. In this paper we present a new approach to bio-sequence database scanning using re-configurable FPGA-based hardware platforms to gain high performance at low cost. Efficient mappings of the Smith-Waterman algorithm using fine-grained parallel processing elements (PEs) that are tailored towards the parameters of a query have been designed. We use customization opportunities available at run-time to dynamically hyper customize the systolic array to make better use of available resource. Our FPGA implementation achieves a speedup of approximately 170 for linear gap penalties and 125 for affine gap penalties as compared to a standard desktop computing platform. We show how hyper-customization at run-time can be used to further improve the performance.
Starting Page	229
Ending Page	237
Page Count	9
File Format	PDF
ISBN	1595930299
DOI	10.1145/1046192.1046222
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2005-02-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Smith-waterman Bio-informatics Dynamic re-configuration Fpga
Content Type	Text
Resource Type	Article

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