Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2

Abstract miRNAs comprise an abundant class of small non‐coding RNAs that play important roles in a wide range of biological processes by post‐transcriptional regulation of a large fraction of animal genes. High‐throughput sequencing machines and the availability of completely sequenced genomes make it possible to reliably identify miRNAs with computational methods. This unit documents how to use the miRDeep2 software package to identify novel and known microRNAs in small RNA deep‐sequencing data. Moreover, the usage of miRDeep2 to profile miRNA expression across samples is illustrated. Curr. Protoc. Bioinform . 36:12.10.1‐12.10.15. © 2011 by John Wiley & Sons, Inc.