Efficient drawing of RNA secondary structure

In this paper, we propose a new layout algorithm that draws the secondary structure of a Ribonucleic Acid (RNA) automatically according to some of the biologists’ aesthetic criteria. Such layout insures that two equivalent structures (or sub-structures) are drawn in a same and planar way. In order to allow a visual comparison of two RNAs, we use an heuristic that places the biggest similar part of the two structures in the same position and orientation. Article Type Communicated by Submitted Revised Regular paper M. T. Goodrich March 2005 June 2006 Research supported in part by ACI Masse de données, Navgraph project. D. Auber et al., RNA secondary structure, JGAA, 10(2) 329–351 (2006) 330