Computational Prediction of MicroRNA Genes

  • Jana Hertel
  • David Langenberger
  • Peter F. Stadler
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)

Abstract

The computational identification of novel microRNA (miRNA) genes is a challenging task in bioinformatics. Massive amounts of data describing unknown functional RNA transcripts have to be analyzed for putative miRNA candidates with automated computational pipelines. Beyond those miRNAs that meet the classical definition, high-throughput sequencing techniques have revealed additional miRNA-like molecules that are derived by alternative biogenesis pathways. Exhaustive bioinformatics analyses on such data involve statistical issues as well as precise sequence and structure inspection not only of the functional mature part but also of the whole precursor sequence of the putative miRNA. Apart from a considerable amount of species-specific miRNAs, the majority of all those genes are conserved at least among closely related organisms. Some miRNAs, however, can be traced back to very early points in the evolution of eukaryotic species. Thus, the investigation of the conservation of newly found miRNA candidates comprises an important step in the computational annotation of miRNAs.

Topics covered in this chapter include a review on the obvious problem of miRNA annotation and family definition, recommended pipelines of computational miRNA annotation or detection, and an overview of current computer tools for the prediction of miRNAs and their limitations. The chapter closes discussing how those bioinformatic approaches address the problem of faithful miRNA prediction and correct annotation.

Key words

miRNA Machine learning Homology Structure conservation 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jana Hertel
    • 1
  • David Langenberger
    • 1
  • Peter F. Stadler
    • 2
    • 3
    • 4
    • 5
    • 6
    • 7
  1. 1.Bioinformatics Group, Department of Computer ScienceUniversity of LeipzigLeipzigGermany
  2. 2.Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  3. 3.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  4. 4.Fraunhofer Institute for Cell Therapy and ImmunologyLeipzigGermany
  5. 5.Institute for Theoretical Chemistry, University of ViennaViennaAustria
  6. 6.Center for non-coding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark
  7. 7.Santa Fe InstituteSanta FeUSA

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