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.