Predicting Secondary Structures Common to Two RNA Sequences
Speaker: David Matthews, MD PhD , University of Rochester Medical Center
Date: May 2 2005
Time: 11:30AM to 1:00PM
Location: STAR 32-D463
Host: P Clote/ BC & B Berger/ MIT, MIT
Contact: Kathleen Dickey, 617 253-3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/****PLEASE note location****
Dynalign is a dynamic programming algorithm that finds the lowest free energy secondary structure common to two, unaligned sequences and the sequence alignment that facilitates that structure. Recently, Dynalign has been extended to the prediction of a set of low energy structures. On average, secondary structures predicted by Dynalign are significantly more accurate than secondary structures predicted using a single sequence.
The talk will present the free energy nearest neighbor model for predicting RNA secondary structure stability. The dynamic programming recursions for predicting the set of low energy structures will be discussed. Finally, recently implemented heuristics to speed the calculation will be presented.
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