RNASurface

Welcome to RNASurface web-server!

RNA sequence may contain regulatory secondary structures. These structures have low free energy and specific pattern of probing data (SHAPE, PARS, DMS, etc).
RNASurface is designed to analyze structured segments in RNA sequences. It uses unified measure (Z-score) to reflect significance of secondary structure, taking into account free energy and probing data (if available). RNASurface calculates Z-score of each RNA segment for long sequences and provides heatmap visualization of these Z-scores coupled with detected structured RNA elements.
Results could be download in a BED or WIG formats to further use it as custom tracks in genome browsers.

To get started with RNASurface click 'RUN' tab or here.
Standalone programs are available here.
Overview of the method and web-server instructions can be found here




If you find RNASurface useful, please cite us:

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. Ruslan A. Soldatov; Svetlana V. Vinogradova; Andrey A. Mironov. Bioinformatics 2013; doi: 10.1093/bioinformatics/btt701