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article · 2005

Using Graphics Hardware to Accelerate Biological Sequence Database Scanning

Gerrit Voß, Wolfgang Müller‐Wittig, Bertil Schmidt, Andre Schroder

Cited by 4Abstract and details only

Abstract

Sequence alignment is a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases. In this paper we present a new approach to high performance biological sequence database scanning on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by then- enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have reformulated the Smith-Waterman dynamic programming algorithm in terms of computer graphics primitives. This results in an implementation with significant runtime savings on two standard off-the-shelf computer graphics cards. To our knowledge this is the first reported mapping of biological sequence alignment onto a graphics processing unit.

Cite this paper

APA 7

Voß, G., Müller‐Wittig, W., Schmidt, B., & Schroder, A. (2005). Using Graphics Hardware to Accelerate Biological Sequence Database Scanning. https://doi.org/10.1109/tencon.2005.300995

MLA 9

Voß, Gerrit, et al. “Using Graphics Hardware to Accelerate Biological Sequence Database Scanning.” 2005, pp. 1–6, https://doi.org/10.1109/tencon.2005.300995.

Chicago

Voß, Gerrit, Wolfgang Müller‐Wittig, Bertil Schmidt, and Andre Schroder. 2005. “Using Graphics Hardware to Accelerate Biological Sequence Database Scanning.” https://doi.org/10.1109/tencon.2005.300995.

Harvard

Voß, G. et al. (2005) ‘Using Graphics Hardware to Accelerate Biological Sequence Database Scanning’. Available at: https://doi.org/10.1109/tencon.2005.300995.

BibTeX
@article{vo2005using,
  title = {{Using Graphics Hardware to Accelerate Biological Sequence Database Scanning}},
  author = {Voß, Gerrit and Müller‐Wittig, Wolfgang and Schmidt, Bertil and Schroder, Andre},
  pages = {1--6},
  year = {2005},
  doi = {10.1109/tencon.2005.300995}
}

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