Benchmarking RNA secondary structure comparison algorithms

Since the last ten years several tools have been proposed for RNA secondary structure pairwise comparison. These tools use different models (ordered tree or forest, arc annotated sequence, multi-level tree) and methods (edit distance, alignment). We present a first benchmark on these tools. For various RNA families, we built two sets of secondary structures. The first, called the reference set, is composed of a small number of RNAs with their known structures. The second is composed of sequences folded using Mfold and RNAshapes. Some of these sequences correspond to structural RNAs of the same families (true events), other correspond to noise. We study the ability of each tool to find the true events using the reference set. In particular we focus on the results in term of sensibility/specificity, on the spreading of the scores and on the time of computation.