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 http://rnaspace.org 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.
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA, RNA, 17(11):1947-56, Nov. 2011.
Poster, JOBIM Paris, June 2011.
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)
PF SIGENAE, INRA Toulouse
IGM, UMR 8621 CNRS - Univ. Paris Sud
This work was supported in 2007 by the RNG and in 2010 by ReNaBI (french National Network of Genomic Centers).