A Practical Guide to miRNA Target Prediction

  • Most Mauluda Akhtar
  • Luigina Micolucci
  • Md Soriful Islam
  • Fabiola Olivieri
  • Antonio Domenico Procopio
Part of the Methods in Molecular Biology book series (MIMB, volume 1970)


MicroRNAs (miRNAs) are small endogenous noncoding RNA molecules that posttranscriptionally regulate gene expression. Since their discovery, a huge number of miRNAs have been identified in a wide range of species. Through binding to the 3′ UTR of mRNA, miRNA can block translation or stimulate degradation of the targeted mRNA, thus affecting nearly all biological processes. Prediction and identification of miRNA target genes is crucial toward understanding the biology of miRNAs. Currently, a number of sophisticated bioinformatics approaches are available to perform effective prediction of miRNA target sites. In this chapter, we present the major features that most algorithms take into account to efficiently predict miRNA target: seed match, free energy, conservation, target site accessibility, and contribution of multiple binding sites. We also give an overview of the frequently used bioinformatics tools for miRNA target prediction. Understanding the basis of these prediction methodologies may help users to better select the appropriate tools and analyze their output.

Key words

MicroRNA Target prediction Seed match Conservation Free energy Site accessibility Bioinformatic tools 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Most Mauluda Akhtar
    • 5
  • Luigina Micolucci
    • 1
    • 2
  • Md Soriful Islam
    • 3
  • Fabiola Olivieri
    • 1
    • 4
  • Antonio Domenico Procopio
    • 1
    • 4
  1. 1.Laboratory of Experimental Pathology, Department of Clinical and Molecular SciencesUniversità Politecnica delle MarcheAnconaItaly
  2. 2.Computational Pathology Unit, Department of Clinical and Molecular SciencesUniversità Politecnica delle MarcheAnconaItaly
  3. 3.Department of Gynecology and ObstetricsJohns Hopkins University, School of MedicineBaltimoreUSA
  4. 4.Center of Clinical Pathology and Innovative TherapiesItalian National Research Center on Aging (INRCA-IRCCS)AnconaItaly
  5. 5.BioinformaticsAsian University for WomenChattogramBangladesh

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