Sequence to Structure (S2S): display, manipulate and interconnect RNA data from the sequence to the structure

01-15-2008: Happy new year !! 2008 will be the year of the new versions of S2S, Assemble and their underlying framework named PARADISE. These tools are hosted by the Simtk website. At now, no official release, but everything is available in the Subversion repository. A wiki under heavy construction is also available here. Starting from now, the bioinformatics.org website for S2S is not anymore supported. 11-08-2007: During The new RNA frontiers symposium, I have presented a poster describing the new version of S2S that will be released in few weeks. The poster is available as a PDF file. Be careful, it's a high-quality file (2,7Mb). 01-04-2007: Happy new year !! If like me, you're using MacOSX and you experienced some problems to link PyMOL to S2S using the MacPyMOL or PyMOLX11Hybrid releases, use the third option. Download the equivalent of the standard Linux PyMOL and install it where you want. Once the setup.sh command launched as explained on their website, go to your S2S directory, type "java -jar ./lib/s2s.jar" and fill the "3D Viewer Tool" field to register the pymol file generated by the setup.sh command. And enjoy !! (don't forget to launch X11 before if you want to see your PyMOL application!!) 10-30-2006: more than one year without any news. During this time, two projects related to S2S have been started and are under active development. The first one is named "Assemble". Assemble proposes a graphical framework which allows ab initio construction of complex three-dimensional RNA structures. S2S and Assemble are sub-projects of a larger one which goal is to develop a distributed environment to interconnect tools allowing the production, visualization and manipulation of RNA data. This project, named P.A.R.A.D.I.S.E, is still under heavy construction. We're hoping a first release candidate by the middle of 2007. The PARADISE project will federate the S2S and Assemble sub-projects. 07-22-2005: release of the beta 5 version. I wasn't able to fix the javadoc for this release because I still need to modify several minor things in my code. So perhaps for the next release... 07-19-2005: S2S is the current Projet Spotlight at Bioinformatics.org. According to J.W. Bizzaro, president of the Bioinformatics.org organization, S2S is currently the most popular download. Very nice !! :) 07-18-2005: release of the beta 4 version. 07-14-2005: The article "Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure" is now published in the volume 21, issue 15 (August 1, 2005) of the Bioinformatics journal. You need a subscription to the journal to download the full text article. 06-30-2005: release of the beta 3 version. 05-19-2005: online access to the abstract and full text of the S2S publication 05-19-2005: release of the beta 2 version 05-17-2005: the publication titled "Sequence to Structure (S2S) : display, manipulate and interconnect RNA data from sequence to structure" has been accepted for publication in the Bioinformatics journal 03-08-2005: release of the beta 1 version

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

For any problems, questions, suggestions or comments, post a message to the discussion forums or send a message to f.jossinet{at}ibmc.u-strasbg.fr. This work was supported by a grant from the Action Concertée Incitative Informatique, Mathématique et Physique en Biologie Moléculaire (Ministère de la Recherche-CNRS) and is hosted by the Bioinformatics Organization, Inc.

If you find S2S useful we ask that you cite the following publication:
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
Jossinet F, Westhof E.
Bioinformatics. 2005 Aug 1;21(15):3320-1.

• User's guide : a complete description of the S2S functions
• Technical documentation
• How to hack S2S ?

S2S is developed using Java language and has been tested on Linux and MacOSX machines. You need at least the 1.3 JRE/JSDK version to run it.

S2S uses :

• PyMOL as default 3D viewer. To install this tool, please go to the PyMOL Website
• RNAVIEW as the default algorithm to calculate a secondary structure from a PDB file
• the JDOM and Wutka DTD parser libraries to parse RnaML files
• Jython as scripting tool
• the Dean S. Jones' Icon Collection

S2S is in the public domain. It is not copyrighted. You may freely modify, redistribute or use it for any purpose. Since S2S is provided at no cost in the public domain, in no event shall we be liable to any party for direct, indirect, special, incidental or consequential damages arising out of the use of the S2S application. S2S is provided "as is" without warranty of any kind.

By downloading and installing files related to this project, you agree with the S2S licensing rules above. To download the last version of S2S, go there.

• Step 1 : download and install the RNAVIEW tool as explained at the Nucleic Acid Database WebSite

  [Note to MacOSX users : S2S provides the rnaview executable file compiled under OSX in its "support" directory. If you don't have the Apple Developper tools or if you don't know how to recompile RNAVIEW under OSX, substitute the original "rnaview" file in its "bin" subdirectory with the "rnaview_osx" renamed as "rnaview". Set its executable right for the user (chmod u+x ./rnaview). ]

• Step 2 : download and install the PyMOL application as explained at the PyMol WebSite. If you're using MacOSX, I suggest you to use option 3. I experienced some problems with MacPyMOL and PyMOLX11Hybrid.
• Step 3 : Once the S2S archive downloaded, unzip it by typing in a shell :
  tar -xzvf S2S_XX.tar.gz
  If you are using MacOSX, the unzip step should be done automatically by your operating system using something like Stuffit Expander. The unzip step will create an S2S directory. Put it in an area where you have rights to write files (S2S needs to create some files).
• Step 4 : open a terminal, go in the S2S directory and type :
  java -jar ./lib/s2s.jar
• Step 5 : in the S2S configuration window, choose the "rnaview" executable file as the 3D=>2D tool and your PyMOL executable file as the 3DViewer tool

  Exemple for Mac OS X :
  

  

• Step 6 : type ./s2s.sh start in your terminal from the S2S directory and enjoy S2S !!
• Optional step : to be able to launch S2S from any directory, add the S2S home directory to your PATH

If you want to use S2S as an external library, you need to pass the S2S directory to the java interpreter like :

java -DS2S_HOME=$S2S_HOME

• It looks like S2S is in beta. What doest it mean? Will it ever come out of beta?

We're releasing S2S in beta to get feedback from the bioinformatics and RNA communities. We expect to update the S2S features based on this feedback, and once we're confident the users are satisfied with the features and stability of S2S, the beta label will be removed. Consequently, you should expect some changes in upcoming versions of the product.

We are developing :

• a new Java 3D viewer allowing 3D modeling. This widget will perhaps become the default 3D viewer for S2S. Go to the Assemble website to take a look at this project
• new ways to connect S2S to external programs (like RNAVIEW). We are trying to wrap these external programs as Web Services. Go to the P.A.R.A.D.I.S.E. website to take a look at this project.

	A beta3 S2S screenshot displaying the 2D and 3D structures of the Haloarcula marismortui large ribosomal subunit (NDBID : RR0033)
	A beta3 S2S screenshot displaying the Thermus thermophilus RnaseP 3D structure from Krasilnikov et al (2004) (PDBID : 1U9S, NDBID : UR0040)
	A beta3 S2S screenshot displaying the Thermus thermophilus RnaseP 3D structure from Krasilnikov et al (2004) (PDBID : 1U9S, NDBID : UR0040)
	A beta1 S2S screenshot displaying the SARS s2m 3D structure from Robertson et al (2005) in

Until the release of the 1.0 stable version, the scripts can be incompatible between beta releases. Check the S2S version in the script you want to use.

• Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
• RNAML: a standard syntax for exchanging RNA information.
• Tools for the automatic identification and classification of RNA base pairs
• Geometric nomenclature and classification of RNA base pairs
• The non-Watson-Crick base pairs and their associated isostericity matrices

• NDB WebSite
• RNAVIEW
• The RnaML file format
• RnaMLView
• My french S2S page
• PyMOL WebSite
• Java Technology
• Jython
• JDOM
• Wutka DTD Parser