Fast folding and comparison of RNA secondary structures View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1994-02

AUTHORS

I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster

ABSTRACT

Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are. More... »

PAGES

167-188

References to SciGraph publications

  • 1991-10. Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures in MONATSHEFTE FÜR CHEMIE - CHEMICAL MONTHLY
  • 1990-08. In vitro selection of RNA molecules that bind specific ligands in NATURE
  • 1984-07. General methods of sequence comparison in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1993-04. RNA multi-structure landscapes in EUROPEAN BIOPHYSICS JOURNAL
  • 1984-07. RNA secondary structures and their prediction in BULLETIN OF MATHEMATICAL BIOLOGY
  • Journal

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  • Identifiers

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    http://scigraph.springernature.com/pub.10.1007/bf00818163

    DOI

    http://dx.doi.org/10.1007/bf00818163

    DIMENSIONS

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