Campuses:

Prediction of the Secondary Structure Common to Two Sequences: Free Energy Minimization and Comparative Analysis

Monday, October 29, 2007 - 12:05pm - 12:35pm
EE/CS 3-180
David Mathews (University of Rochester)
In this talk, I will discuss the dynamic programming
methods for
simultaneously predicting secondary structure and alignment
for two
sequences. This approach was first suggested by Sankoff in
1985.
Recently, it has been implemented by several groups, using
one or more
heuristics to reduce the computational cost. Our
implementation,
Dynalign, finds the lowest free energy common secondary
structure. It
uses single sequence secondary structure prediction and
sequence
alignment data as input to reduce the search space to make
the
calculation tractable for long sequences.
MSC Code: 
60G25
Keywords: