CHAPTER 46miRNA Target Prediction

Sarika, Mir Asif Iquebal and D Kumar

CABiN, IASRI, New Delhi


MicroRNAs (miRNAs) are short, non‐coding RNA molecules that function to regulate gene expression post‐transcriptionally. Due to the potential of one miRNA to target multiple gene transcripts, miRNAs are recognized as a primary mechanism to regulate gene expression. MicroRNA targets can be identified by pairing between the miRNA seed region and complementary sites within target mRNAs. Several miRNA target prediction tools, based on different computational approaches (e.g., modeling of physical interactions, machine learning techniques, etc.) are available. These tools include TargetScan, miRanda, and so on.

A common set of rules for miRNA target prediction includes complementarity, free energy calculations and evolutionary arguments and cooperativity of binding.

This chapter aims at predicting mRNA targets of the given microRNAs using various miRNA prediction tools.


This predicts the biological targets of miRNAs by searching for the presence of sites that match the seed region of each miRNA (Agarwal et al., 2015).

46.2.1 Objective

To search for predicted miRNA sequences in the human genome for the gene “HMGA2”.

46.2.2 Procedure

  1. Open the TargetScan web server:
  2. Select the species “Human” and enter the human gene symbol (i.e., HMGA2).
  3. Select the required conditions from the ...

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