Computational Methods for RNA Secondary Structure Determination

Monday, October 29, 2007 - 11:30am - 12:00pm
EE/CS 3-180
Michael Zuker (Rensselaer Polytechnic Institute)
The talk will begin with a definition of RNA secondary structure,
including three different ways to display these structures. Two distinct
approaches will be presented for determining secondary structure from
sequence data. The comparative method requires a multiple sequence
alignment of a collection of homologous RNA sequences. It uses phylogeny
to determine common, conserved base pairs that are more likely to be the
result of evolution than to exist by chance. On the other hand, recursive
algorithms may be used on single sequences to compute minimum free energy
structures, partition functions and other biophysical quantities. These
algorithms ignore evolution and use empirically derived energy parameters
based on physical chemistry. Examples will be given for both methods.