Prediction and differential analysis of RNA secondary structure

Abstract

Background: RNA structure is the crucial basis for RNA function in various cellular processes. Over the last decade, high throughput structure profiling (SP) experiments have brought enormous insight into RNA secondary structure. Results: In this review, we first provide an overview of approaches for RNA secondary structure prediction, including free energy-based algorithms and comparative sequence analysis. Then we introduce SP technologies, databases to document SP data, and pipelines/algorithms to normalize and interpret SP data. Computational frameworks that incorporate SP data in RNA secondary structure prediction are also presented. Conclusions: We finally discuss potential directions for improvement in the prediction and differential analysis of RNA secondary structure.