Introduction

Small interfering RNA (siRNA)-mediated knock-down is a widely used experimental approach to characterizing gene function. Although siRNAs are designed to guide the cleavage of perfectly complementary mRNA targets, acting similarly to microRNAs (miRNAs), siRNAs down-regulate the expression of hundreds of genes to which they have only partial complementarity. Prediction of these siRNA 'off-targets' remains difficult, due to the incomplete understanding of siRNA/miRNA-target interactions. Combining a biophysical model of miRNA-target interaction with structure and sequence features of putative target sites we developed a suite of algorithms, MIRZA-G, for the prediction of miRNA targets and siRNA off-targets on a genome-wide scale. The MIRZA-G variant that uses evolutionary conservation performs better than currently available methods in predicting canonical miRNA target sites and in addition, it predicts non-canonical miRNA target sites with similarly high accuracy. Furthermore, MIRZA-G variants predict siRNA off-target sites with an accuracy unmatched by currently available programs. Thus, MIRZA-G may prove instrumental in the analysis of data resulting from large-scale siRNA screens.

Publications

  1. Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.
    Cite this
    Gumienny R, Zavolan M, 2015-02-01 - Nucleic acids research

Credits

  1. Rafal Gumienny
    Developer

    Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Switzerland

  2. Mihaela Zavolan
    Investigator

    Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Switzerland

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Summary
AccessionBT006377
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionSwitzerland
Submitted ByMihaela Zavolan