Basic Applied Bioinformatics

CHAPTER 45Estimating MicroRNA Expression Using the miRDeep2 Tool

GVPPSR Kumar,, A Kumar and AP Sahoo

Animal Biotechnology Division, IVRI, UP, India

45.1 INTRODUCTION

For detection of miRNA from NGS data, several software tools have been developed to support the data analysis. These include: miRTRAP; DSAP; miRExpress; mirTools; miRDeep; miRNAkey and mireap; miRanalyzer; Mirena, and so on. Among this software, miRDeep and mireap are considered to be the best for prediction of novel miRNAs from mammalian data sets (Li et al., 2012). Here, we will discuss miRDeep (Friedlander et al., 2008, 2012). The codes and associated annotations have been taken from available guidances available online. In several cases, the explanations are verbatim with the source. The source URLs have been duly cited in this chapter.

miRDeep is a tool that helps in identifying miRNAs from the large pool of sequenced transcripts from a deep sequencing run. A probabilistic model is used to take into account the miRNA biogenesis for scoring fitness, and position the RNA sequence with the secondary structure of the miRNA precursor. miRDeep2 is an overhauled version of the original miRDeep algorithm, with added extensive new packages. The accuracy and sensitivity of miRDeep2 are estimated through its internal statistical controls.

Both the canonical and non‐canonical miRNAs in deep sequencing data can be identified through miRDeep2. The miRNA expression profiling across samples can also be done using this tool. ...