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Parallel performance evaluation of multithreaded local sequence alignment

Published: 16 June 2011 Publication History

Abstract

Bioniformatics is area, demanding knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This scientific area requires powerful computing resources for exploring large sets of biological data. Biological sequence processing is a key for molecular biology. Smith-Waterman algorithm, based on dynamic programming has become the most fundamental in bioinformatics. The goal of this paper is to investigate the efficiency of parallel multithreaded implementation based on Smith-Waterman algorithm. Performance parameters have been estimated by the experiments using various data sets on two parallel computer platforms.

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  • (2011)High Performance System Framework for Parallel in-Silico Biological SimulationsProceedings of the 2011 Developments in E-systems Engineering10.1109/DeSE.2011.72(553-557)Online publication date: 6-Dec-2011

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cover image ACM Other conferences
CompSysTech '11: Proceedings of the 12th International Conference on Computer Systems and Technologies
June 2011
688 pages
ISBN:9781450309172
DOI:10.1145/2023607
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

  • TELECVB: TELECOMS - Varna, Bulgaria
  • Austrian Comp Soc: Austrian Computer Society
  • BPCSB: BULGARIAN PUBLISHING COMPANY - Sofia, Bulgaria
  • IOMAIBB: INSTITUTE OF MATHEMATICS AND INFORMATICS - BAS, Bulgaria
  • NBUBB: New Bulgarian University - BAS, Bulgaria
  • Technical University of Sofia
  • IOIACTBB: INSTITUTE OF INFORMATION AND COMMUNICATION TECHNOLOGIES - BAS, Bulgaria
  • TSFPS: THE SEVENTH FRAMEWORK PROGRAMME - SISTER
  • ERSVB: EURORISC SYSTEMS - Varna, Bulgaria
  • FOSEUB: FEDERATION OF THE SCIENTIFIC ENGINEERING UNIONS - Bulgaria
  • UORB: University of Ruse, Bulgaria
  • BBPSB: BULGARIAN BUSINESS PUBLICATIONS - Sofia, Bulgaria
  • CASTUVTB: CYRIL AND ST. METHODIUS UNIVERSITY of Veliko Tarnovo, Bulgaria
  • TECHUVB: Technical University of Varna, Bulgaria
  • LLLPET: LIFELONG LEARNING PROGRAMME - ETN TRICE
  • IEEEBSB: IEEE Bulgaria Section, Bulgaria

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 16 June 2011

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Author Tags

  1. bioniformatics
  2. high performance computing
  3. parallel performance
  4. sequence alignment

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  • Research-article

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CompSysTech '11
Sponsor:
  • TELECVB
  • Austrian Comp Soc
  • BPCSB
  • IOMAIBB
  • NBUBB
  • IOIACTBB
  • TSFPS
  • ERSVB
  • FOSEUB
  • UORB
  • BBPSB
  • CASTUVTB
  • TECHUVB
  • LLLPET
  • IEEEBSB

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Overall Acceptance Rate 241 of 492 submissions, 49%

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Cited By

View all
  • (2011)High Performance System Framework for Parallel in-Silico Biological SimulationsProceedings of the 2011 Developments in E-systems Engineering10.1109/DeSE.2011.72(553-557)Online publication date: 6-Dec-2011

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