Subject: | RNA Secondary Structure Prediction |
Presenter: | Mirela Andronescu |
Paper: | " An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots " |
  | by JRuan, G.D. Stormo, and W. Zhang |
Abstract |
An iterated loop matching approach to the prediction of RNA secondary structures
with pseudoknots
MOTIVATION: Pseudoknots have generally been excluded from the prediction
of RNA secondary structures due to its difficulty in modeling. Although,
several dynamic programming algorithms exist for the prediction of
pseudoknots using thermodynamic approaches, they are neither reliable nor
efficient. On the other hand, comparative methods are more reliable, but
are often done in an ad hoc manner and require expert intervention.
Maximum weighted matching, an algorithm for pseudoknot prediction with
comparative analysis, suffers from low-prediction accuracy in many cases. Reference:
J Ruan, G.D. Stormo, and W. Zhang, "An iterated loop matching approach to
the prediction of RNA secondary structures with pseudoknots",
Bioinformatics 2004, vol. 20 no. 1 pages 58-66.
The paper is available at http://www.cs.wustl.edu/~zhang/projects/rna/ilm/ilm.pdf
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