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Sfold Tools for MicroRNA Target Prediction

  • William Rennie
  • Shaveta Kanoria
  • Chaochun Liu
  • C. Steven Carmack
  • Jun Lu
  • Ye DingEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1970)

Abstract

Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. In this chapter, we describe STarMir and STarMirDB, two application modules of the Sfold RNA package. STarMir is a Web server for performing miRNA binding site predictions for mRNA and target sequences submitted by users. STarMirDB is a database of precomputed transcriptome-scale predictions. Both STarMir and STarMirDB provide comprehensive sequence, thermodynamic, and target structure features, a logistic probability as a measure of confidence for each predicted site, and a publication-quality diagram of the predicted miRNA–target hybrid. In addition, STarMir now offers a new quantitative score to address combined regulatory effects of multiple seed and seedless sites. This score provides a quantitative measure of the overall regulatory effects of both seed and seedless sites on the target. STarMir and STarMirDB are freely available to all through the Sfold Web application server at http://sfold.wadsworth.org.

Key words

miRNA CLIP Target mRNA RNA secondary structure miRNA binding site Efficacy Database Quantitative score 

Notes

Acknowledgments

The Bioinformatics Core at the Wadsworth Center is acknowledged for supporting computing resources for this work. This work is supported in part by the National Institutes of Health (grants GM099811, GM116855 to Y.D. and J. L.).

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Copyright information

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

Authors and Affiliations

  • William Rennie
    • 1
  • Shaveta Kanoria
    • 1
  • Chaochun Liu
    • 1
  • C. Steven Carmack
    • 1
  • Jun Lu
    • 2
  • Ye Ding
    • 1
    Email author
  1. 1.New York State Department of Health, Wadsworth CenterCenter for Medical ScienceAlbanyUSA
  2. 2.Department of Genetics, Yale Stem Cell CenterYale UniversityNew HavenUSA

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