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Open Access Research article

ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins

Sébastien Tempel1, Nicolas Pollet2 and Fariza Tahi1*

Author Affiliations

1 Laboratoire IBISC-IBGBI EA 4526, Université d’Evry-Val d’Essonne, 91034 EVRY, Genopole, 23 Bd de France, France

2 Metamorphosys iSSB, CNRS, Université d’Evry-Val d’Essonne, 91058 Evry, Genopole, Genavenir 3 - Genopole campus 1, 1 rue Pierre Fontaine, France

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BMC Bioinformatics 2012, 13:246  doi:10.1186/1471-2105-13-246

Published: 25 September 2012

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 webcite.