Parametric analysis of RNA folding

TL;DR

This paper introduces a geometric approach to analyze how variations in certain free energy parameters affect RNA secondary structure predictions, using the construction of an RNA polytope.

Contribution

It extends parametric sequence alignment methods to RNA folding, constructing an RNA polytope to study parameter effects on structure predictions.

Findings

Variation of specific parameters has limited impact on predicted structures.

The RNA polytope captures structures with common branching patterns.

Mapping known structures to the polytope aids in understanding structure variability.

Abstract

We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of 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 predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.