UNIVERSITY OF MALTA
LIFE SCIENCE RESEARCH SEMINARS
Web: http://events.um.edu.mt/scisem/
Email: scisem@um.edu.mt
Abstract form
Title: A New Measure for RNA Secondary Structures
Presenter: Ms Phaedra Agius
Contact address: Department of Mathematical Sciences,
316E Rensselaer Polytechnic Institute, Troy NY 12180, USA
Tel: +1-518-312-7335
Fax:
Email: agiusp@rpi.edu
Presentation date: 20th December 2006
Abstract
(approximately 200-250 words)
RNA secondary structures are difficult to predict and hard to compare. Minimum free
energy folds and suboptimal energy folds have been found to be good educated guesses of
the true structures. More recent attempts have focused on computing a random sample of
RNA secondary structures from a sequence using the appropriate software. This sample is
first subjected to the Base Pair Metric to compare them, and then to a
clustering algorithm in search of common underlying groups.
We present a novel algorithm, the Relaxed Base Pair score to compare RNA secondary
structures. We subject our structure samples to spectral clustering methods that yield stable
clusters. We show that the clusters we obtain are more stable and informative than those
obtained using the Base Pair Metric.