Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences

Abstract

Predicting the secondary structures of RNA molecules is an essential step to characterize their functions, but the thermodynamic probability of any prediction is generally small. On the other hand, there are a few tools for calculating and visualizing various secondary structural information from RNA sequences. We implemented a web server that calculates in parallel various features of secondary structures: different types of secondary structure predictions, the marginal probabilities for local structural contexts, accessibilities of the subsequences, the energy changes by arbitrary base mutations, and the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPknot, CapR, Raccess, Rchange, RintD, and RintW.