Efficient RNA sequence manipulations (like multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures like those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information.

S2S proposes a framework in which a user can easily display, manipulate, and interconnect heterogeneous RNA data like multiple sequence alignments, secondary and tertiary structures. It has been implemented with the Java language and has been developed and tested under UNIX systems like Linux and MacOSX.

S2S 1.0 has been published in 2005 in the Bioinformatics journal (Jossinet F. and Westhof E., 2005). This website describes the 2.0 version of S2S.

• 06-15-2009: S2S is now available to anyone. Check the Downloads page.
• 04-30-2009: the "official" beta-testers have received the instructions to download the Release Candidate 1 of S2S 2.0
• 04-14-2009: you can find news and technical details about S2S on the "Serialized Thoughts" blog
• 03-27-2009: the release of S2S 2.0 is planned for the second half of April 2009
• 03-05-2009: the new website is online and under construction. No official release of the new S2S until few weeks. If you want to be an official beta tester, send us an email

• Serialized Thoughts: a blog where you can find news and technical details about S2S
• Assemble: a project complementary to S2S
• PARADISE: S2S and Assemble are constructed over the PARADISE engine. This engine sums up the technologies necessary to construct more easily our tools:
  • the RNA concepts displayed and manipulated (helices, single-strands, tertiary and secondary structures, structural alignments,...)
  • the construction and deployment of a calculation layer embedding RNA algorithms
• The non-Watson-Crick base pairs and their associated isostericity matrices: this publication describes the base-pair symbols used in the 2D scene
• RNAView: generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.
• Vienna RNA Package: several stand-alone programs for the prediction and comparison of RNA secondary structures.
• The Java Agent DEvelopment Framework: used to develop the calculation layer hosting the RNA algorithms
• MyDoggy: the Java docking framework to make the graphical interface of S2S more attractive
• Tango Desktop Project and FamFamFam: the icon sets used for S2S

The S2S project is managed by Dr. Fabrice Jossinet. It is developed in the laboratory of Pr. Eric Westhof at the "Institut de Biologie Moleculaire et Cellulaire" of Strasbourg, France (Team "Architecture et Réactivité de l'ARN", UPR 9002 of CNRS, Université de Strasbourg).