Covariance models are a powerful and popular method for searching genomic databases for new members of functional RNA families. The use of prior information in covariance model parameter estimation is crucial since many RNA families only have a very few known examples or all those that are known are in a sub-family of the actual family. Experimental thermodynamic measurements of RNA structures point to a number of regularities in molecular stability that are not captured in current covariance modeling practice. Among these are the dependence of stability on hairpin closing pair and loop end nucleotide identities and well as hairpin loop length. Preliminary evidence has been found that incorporation of these effects into priors and model structure may improve covariance model performance. It is proposed to investigate additional thermodynamics-inspired improvements to covariance model parameter estimation and structure, combine the prior information with in-family observed- frequency data in an optimal fashion, and to expand testing of the performance of the model structure changes and parameter estimation methods.

Public Health Relevance

This project improves the effectiveness of programs which search genomic databases for genes which specify RNA molecules which have biological function without conversion into protein. These molecules are involved in human disease and aging processes. Finding additional genes of this class will improve the ability to design drug and other therapies for human disease and age-related health degeneration.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Academic Research Enhancement Awards (AREA) (R15)
Project #
1R15GM087646-01
Application #
7638375
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Preusch, Peter C
Project Start
2009-07-01
Project End
2014-03-31
Budget Start
2009-07-01
Budget End
2014-03-31
Support Year
1
Fiscal Year
2009
Total Cost
$211,500
Indirect Cost
Name
Boise State University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
072995848
City
Boise
State
ID
Country
United States
Zip Code
83725