RNAspace is an environment that allows to create web sites dedicated to non-protein-coding RNA (ncRNA) prediction, annotation and analysis. The web sites allow users to run a variety of tools in an integrated and flexible way. RNAspace is focused on the integration of complementary ncRNA gene finders. It also offers a set of tools for the comparison, visualization, edition and export of ncRNAs candidates. Predictions can be filtered according to a large set of characteristics.

A public web site has been created that allows for on line annotation of a complete bacterial genome or a small eukaryotic chromosome.

It has been conceived to be as parameterizable and extensible as possible. This allows to configure web sites for special uses: A site dedicated to a species with limited accesses, a site shared by a group of biologists ...
Parametrization of a site includes declaration of available gene-finders, limits for process time execution, disk space, storage duration, execution on a connected computer cluster via a job scheduler.
It is also worth to note that the environment could be used in command line and thus inserted in a pipeline.

Communication An integrated environment for the prediction, annotation, and analysis of ncRNA, RNA, 17(11):1947-56, Nov. 2011.

Poster, JOBIM Paris, June 2011.

Technical points

The environment relies on collaboratively-developed code using the Python language and the HTTP framework CherryPy.
The code is open source under GPL license and is available on Source Forge.


Unité de Biométrie et Intelligence Artificielle, INRA Toulouse
Marie-Josée Cros, Christine Gaspin
BONSAI team, LIFL - UMR CNRS 8022 - Univ. Lille 1 and INRIA Lille Nord Europe
Benjamin Grenier-Boley (2008), Antoine de Monte (2008-2010), Laurie Tonon (2010-2011), Hélène Touzet
PF Bioinformatique, INRA Toulouse
Christine Gaspin, J-Marc Larré (2008), Jérôme Mariette, Guilhem Richard (2010)
Philipe Bardou
IGM, UMR 8621 CNRS - Univ. Paris Sud
Daniel Gautheret


This work was supported in 2007 by the RNG and in 2010 by ReNaBI (french National Network of Genomic Centers).