Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing

Abstract

Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified. Here, we will present workflows to predict viroid structures and draw the predicted structures in a pleasing and descriptive way using recently developed software.

Keywords: ConStruct; Consensus structure; Partition folding; R2R; RNAalifold; RNAfold; Sequence and structure drawing; Structure of minimum free energy; VARNA.