title: RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.
abstract: The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene finders and a set of tools for the comparison, visualization, editing, and export of ncRNA candidates. Predictions can be filtered according to a large set of characteristics. Based on this environment, we created a public website located at http://RNAspace.org. It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project (http://rnaspace.sourceforge.net/).
authors.affiliation: INRA, UBIA, UR 875, F-31320 Castanet-Tolosan, France.
authors.forename: Marie-Josée
authors.initials: MJ
authors.lastname: Cros
authors.forename: Antoine
authors.initials: A
authors.lastname: de Monte
authors.forename: Jérôme
authors.initials: J
authors.lastname: Mariette
authors.forename: Philippe
authors.initials: P
authors.lastname: Bardou
authors.forename: Benjamin
authors.initials: B
authors.lastname: Grenier-Boley
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
authors.forename: Hélène
authors.initials: H
authors.lastname: Touzet
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016678:Genome; D020407:Internet; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000032:analysis* / Q000737:chemistry; D012984:Software
chemical_list: D022661:RNA, Untranslated