title: Computational prediction of the localization of microRNAs within their pre-miRNA.
abstract: MicroRNAs (miRNAs) are short RNA species derived from hairpin-forming miRNA precursors (pre-miRNA) and acting as key posttranscriptional regulators. Most computational tools labeled as miRNA predictors are in fact pre-miRNA predictors and provide no information about the putative miRNA location within the pre-miRNA. Sequence and structural features that determine the location of the miRNA, and the extent to which these properties vary from species to species, are poorly understood. We have developed miRdup, a computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA. MiRdup is based on a random forest classifier trained with experimentally validated miRNAs from miRbase, with features that characterize the miRNA-miRNA* duplex. Because we observed that miRNAs have sequence and structural properties that differ between species, mostly in terms of duplex stability, we trained various clade-specific miRdup models and obtained increased accuracy. MiRdup self-trains on the most recent version of miRbase and is easy to use. Combined with existing pre-miRNA predictors, it will be valuable for both de novo mapping of miRNAs and filtering of large sets of candidate miRNAs obtained from transcriptome sequencing projects. MiRdup is open source under the GPLv3 and available at http://www.cs.mcgill.ca/∼blanchem/mirdup/.
authors.affiliation: School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada H3A2B2 and Laboratoire de bioinformatique du département informatique, Université du Québec À Montréal, Montreal, Quebec, Canada H2X3Y7.
authors.forename: Mickael
authors.initials: M
authors.lastname: Leclercq
authors.forename: Abdoulaye Banire
authors.initials: AB
authors.lastname: Diallo
authors.forename: Mathieu
authors.initials: M
authors.lastname: Blanchette
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D009690:Nucleic Acid Conformation; D010944:Plants / Q000235:genetics; D012322:RNA Precursors / Q000032:analysis* / Q000235:genetics; D018749:RNA, Plant / Q000032:analysis* / Q000235:genetics; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant