title: ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins.
abstract: BACKGROUND
  Inverted repeat genes encode precursor RNAs characterized by hairpin structures. These RNA hairpins are then metabolized by biosynthetic pathways to produce functional small RNAs. In eukaryotic genomes, short non-autonomous transposable elements can have similar size and hairpin structures as non-coding precursor RNAs. This resemblance leads to problems annotating small RNAs.
  
  
  RESULTS
  We mapped all microRNA precursors from miRBASE to several genomes and studied the repetition and dispersion of the corresponding loci. We then searched for repetitive elements overlapping these loci. We developed an automatic method called ncRNAclassifier to classify pre-ncRNAs according to their relationship with transposable elements (TEs). We showed that there is a correlation between the number of scattered occurrences of ncRNA precursor candidates and the presence of TEs. We applied ncRNAclassifier on six chordate genomes and report our findings. Among the 1,426 human and 721 mouse pre-miRNAs of miRBase, we identified 235 and 68 mis-annotated pre-miRNAs respectively corresponding completely to TEs.
  
  
  CONCLUSIONS
  We provide a tool enabling the identification of repetitive elements in precursor ncRNA sequences. ncRNAclassifier is available at http://EvryRNA.ibisc.univ-evry.fr.
authors.affiliation: Laboratoire IBISC-IBGBI EA 4526, Université d'Evry-Val d'Essonne, Genopole, 91034 EVRY, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tempel
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pollet
authors.forename: Fariza
authors.initials: F
authors.lastname: Tahi
mesh_terms: D000818:Animals; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020071:Interspersed Repetitive Sequences; D055029:Inverted Repeat Sequences; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D012322:RNA Precursors / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000145:classification / Q000235:genetics; D051381:Rats; D012984:Software
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D058727:RNA, Small Untranslated