Computational approaches for RNA energy parameter estimation.
RNA
; 16(12): 2304-18, 2010 Dec.
Article
in En
| MEDLINE
| ID: mdl-20940338
ABSTRACT
Methods for efficient and accurate prediction of RNA structure are increasingly valuable, given the current rapid advances in understanding the diverse functions of RNA molecules in the cell. To enhance the accuracy of secondary structure predictions, we developed and refined optimization techniques for the estimation of energy parameters. We build on two previous approaches to RNA free-energy parameter estimation (1) the Constraint Generation (CG) method, which iteratively generates constraints that enforce known structures to have energies lower than other structures for the same molecule; and (2) the Boltzmann Likelihood (BL) method, which infers a set of RNA free-energy parameters that maximize the conditional likelihood of a set of reference RNA structures. Here, we extend these approaches in two main ways We propose (1) a max-margin extension of CG, and (2) a novel linear Gaussian Bayesian network that models feature relationships, which effectively makes use of sparse data by sharing statistical strength between parameters. We obtain significant improvements in the accuracy of RNA minimum free-energy pseudoknot-free secondary structure prediction when measured on a comprehensive set of 2518 RNA molecules with reference structures. Our parameters can be used in conjunction with software that predicts RNA secondary structures, RNA hybridization, or ensembles of structures. Our data, software, results, and parameter sets in various formats are freely available at http//www.cs.ubc.ca/labs/beta/Projects/RNA-Params.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA
/
Statistics as Topic
/
Computational Biology
/
Energy Metabolism
Type of study:
Diagnostic_studies
/
Evaluation_studies
/
Prognostic_studies
Limits:
Animals
/
Humans
Language:
En
Journal:
RNA
Journal subject:
BIOLOGIA MOLECULAR
Year:
2010
Document type:
Article
Affiliation country:
United States