Addressing the major limitations of RNA secondary structure prediction software - Talk by Brent Znosko, Saint Louis University

Speaker:  Brent M. Znosko, Associate Professor, Saint Louis University

Title:  Addressing the Major Limitations of RNA Secondary Structure Prediction Software

Abstract:

There are several methods available to predict RNA secondary structure from sequence. The most popular approach is to predict the lowest free energy structure with a dynamic programming algorithm. Surprisingly, there are many RNA structures that are still predicted rather poorly, suggesting that there is still room for improvement. Three limitations of RNA secondary structure prediction software have been identified and addressed: (1) frequently occurring RNA secondary structure motifs were identified and thermodynamically characterized, and updated models were derived, (2) the effect of Na⁺ concentration on the thermodynamic parameters for Watson-Crick pairs was determined and correction factors were derived, and (3) nearest neighbor parameters for common non-standard nucleotides were derived. Free energy parameters, correction factors, and predictive models based on these data can be incorporated into prediction software to improve prediction of RNA secondary structure from sequence.

Bio: 

Brent Znosko earned his BS degree in chemistry from Allegheny College in Meadville, PA and his MS and PhD degrees in chemistry from the University of Rochester in Rochester, NY working in the lab of Doug Turner.  In 2004, he joined the Department of Chemistry at Saint Louis University and is now an Associate Professor.