title: LeARN: a platform for detecting, clustering and annotating non-coding RNAs.
abstract: BACKGROUND
  In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs) in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules.
  
  
  RESULTS
  LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation.
  
  
  CONCLUSIONS
  This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN.
authors.affiliation: Laboratoire Interactions Plantes Micro-organismes UMR441/2594, INRA/CNRS, F-31320 Castanet Tolosan, France. Celine.Noirot@toulouse.inra.fr
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.forename: Thomas
authors.initials: T
authors.lastname: Schiex
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D003628:Database Management Systems; D030561:Databases, Nucleic Acid / Q000458:organization & administration; D020745:Genome, Archaeal; D023281:Genomics / Q000379:methods; D051188:Knowledge Bases; D005810:Multigene Family; D010363:Pattern Recognition, Automated; D043903:Pyrococcus abyssi / Q000235:genetics; D020027:Pyrococcus furiosus / Q000235:genetics; D043902:Pyrococcus horikoshii / Q000235:genetics; D022661:RNA, Untranslated / Q000032:analysis*; D016415:Sequence Alignment; D019712:Thermococcus / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D022661:RNA, Untranslated