Folding RNA on the Cray-2

  • Authors:

  • Michael Ess

  • Affiliations:

  • Cray Computer Corporation, P.O. Box 17500, Colorado Springs, Colorado

  • Venue:
  • Proceedings of the 1990 ACM/IEEE conference on Supercomputing
  • Year:
  • 1990

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Abstract

Predicting RNA folding is a very computationally intensive task, that depends heavily on the assumptions of the model of folding. The 'stem list method' provides a flexible framework to change the assumptions of the model, but the price for this flexibility is its large computational costs. A C implementation of the 'stem list method' is given for the Cray-2 that takes advantage of both vectorization and multi-tasking. This implementation of exhaustive, depth first searching may have uses in other applications.