Accelerating a charged single α-helix search algorithm in protein sequences using FPGA

Zoltán Nagy, Zoltán Gáspári, Ákos Kovács

Research output: Conference contribution

2 Citations (Scopus)

Abstract

Processing and analyzing the immense amount of biological data generated each day requires fast and accurate bioinformatics algorithms. The main characteristic of the these algorithms is the low precision input data which can be stored on 2-5bits. Therefore reconfigurable architectures can be used more efficiently compared to conventional 32 or 64 bit microprocessors, because the accuracy of the functional units can be customized and a relatively small amount of configurable logic is required. In the paper a new architecture is introduced and implemented on FPGA to speed-up a structural motif search algorithm. The architecture can be implemented on a versatile medium range FPGA providing about two orders of magnitude speedup. The system can be efficiently scaled to process several sequences in parallel on a larger FPGA resulting in even higher speedup.

Original languageEnglish
Title of host publicationCNNA 2016 - 15th International Workshop on Cellular Nanoscale Networks and Their Applications
EditorsRonald Tetzlaff
PublisherIEEE Computer Society
Pages117-118
Number of pages2
ISBN (Electronic)9783800742523
Publication statusPublished - jan. 1 2016
Event15th International Workshop on Cellular Nanoscale Networks and Their Applications, CNNA 2016 - Dresden, Germany
Duration: aug. 23 2016aug. 25 2016

Publication series

NameInternational Workshop on Cellular Nanoscale Networks and their Applications
Volume2016-August
ISSN (Print)2165-0160
ISSN (Electronic)2165-0179

Conference

Conference15th International Workshop on Cellular Nanoscale Networks and Their Applications, CNNA 2016
CountryGermany
CityDresden
Period8/23/168/25/16

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Electrical and Electronic Engineering

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  • Cite this

    Nagy, Z., Gáspári, Z., & Kovács, Á. (2016). Accelerating a charged single α-helix search algorithm in protein sequences using FPGA. In R. Tetzlaff (Ed.), CNNA 2016 - 15th International Workshop on Cellular Nanoscale Networks and Their Applications (pp. 117-118). (International Workshop on Cellular Nanoscale Networks and their Applications; Vol. 2016-August). IEEE Computer Society.