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This resemblance leads to problems annotating small RNAs.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>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.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We provide a tool enabling the identification of repetitive elements in precursor ncRNA sequences. ncRNAclassifier is available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/EvryRNA.ibisc.univ-evry.fr\" ext-link-type=\"uri\">http:\/\/EvryRNA.ibisc.univ-evry.fr<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-246","type":"journal-article","created":{"date-parts":[[2012,9,26]],"date-time":"2012-09-26T00:15:09Z","timestamp":1348618509000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins"],"prefix":"10.1186","volume":"13","author":[{"given":"S\u00e9bastien","family":"Tempel","sequence":"first","affiliation":[]},{"given":"Nicolas","family":"Pollet","sequence":"additional","affiliation":[]},{"given":"Fariza","family":"Tahi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,9,25]]},"reference":[{"key":"5441_CR1","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1007\/s00438-010-0556-1","volume":"284","author":"K Miyoshi","year":"2010","unstructured":"Miyoshi K, Miyoshi T, Siomi H: Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. 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