Parallel multiprocessor approaches to the RNA folding problem

  • Authors:

  • Étienne Ogoubi;David Pouliot;Marcel Turcotte;Abdelhakim Hafid

  • Affiliations:

  • Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec, Canada;Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec, Canada;School of Information Technology and Engineering, University of Ottawa, Ottawa, Ontario, Canada;Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, Québec, Canada

  • Venue:
  • PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
  • Year:
  • 2007

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Abstract

To quickly and efficiently fold long ribonucleic acid (RNA) sequences, fast computational models are needed. This paper compares two parallel multiprocessor computer architectures for the prediction of RNA secondary structure. We show promising experimental results using the OpenMP programming environment. This work is intended to be a testbed for the development of new approaches for the prediction of consensus RNA secondary structure from multiple sequences.