UNIT 12.10 Identification of Novel and Known miRNAs in Deep-Sequencing Data with miRDeep2

  1. Sebastian D. Mackowiak

Published Online: 1 DEC 2011

DOI: 10.1002/0471250953.bi1210s36

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Mackowiak, S. D. 2011. Identification of Novel and Known miRNAs in Deep-Sequencing Data with miRDeep2. Current Protocols in Bioinformatics. 36:12.10:12.10.1–12.10.15.

Author Information

  1. Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany

Publication History

  1. Published Online: 1 DEC 2011
  2. Published Print: DEC 2011


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.


  • miRDeep2;
  • miRNA;
  • microRNA;
  • gene prediction;
  • sequencing;
  • expression;
  • profiling