In Silico Prediction of RNA Secondary Structure

Methods Mol Biol. 2017:1543:145-168. doi: 10.1007/978-1-4939-6716-2_7.


The secondary structure of an RNA molecule represents the base-pairing interactions within the molecule and fundamentally determines its overall structure. In this chapter, we overview the main approaches and existing tools for predicting RNA secondary structures, as well as methods for identifying noncoding RNAs from genomic sequences or RNA sequencing data. We then focus on the identification of a well-known class of small noncoding RNAs, namely microRNAs, which play very important roles in many biological processes through regulating post-transcriptionally the expression of genes and which dysregulation has been shown to be involved in several human diseases.

Keywords: Integrative approach; MicroRNA; Noncoding RNA; Pseudoknots; RNA identification; RNA secondary structure; RNA secondary structure prediction.

Publication types

  • Review

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Computer Simulation
  • Humans
  • Models, Molecular*
  • Nucleic Acid Conformation*
  • RNA / chemistry*


  • RNA