Parametric Analysis of RNA Branching Configurations

Valerie Hower, Christine E. Heitsch
2011 Bulletin of Mathematical Biology  
Motivated by recent work in parametric sequence alignment, we study the parameter space for scoring RNA folds and construct an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures
more » ... edicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.
doi:10.1007/s11538-010-9607-3 pmid:21207176 fatcat:ruxbybk26vg35cxhyehxfkm24e