The Circular Secondary Structure Base Pair Probabilities Plot (CS²BP²-Plot) facilitates pairwise comparison of secondary structures for short RNA and DNA sequences up to 200 bases long. CS²BP²-Plot first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAFold version 2.4.6 from the ViennaRNA package version 2.0. Then it provides a two panel comparative view that includes CS²BP²-Plots along with traditional graph, planar and circular diagrams obtained with VARNA version 3-93. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences.

Chimp and Denisovan Human/Highly Accelerated Region 1 (HAR1) RNAs.

To appear