Unit

UNIT 12.1 An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNAi Design

  1. Gary D. Stormo

Published Online: 1 MAR 2006

DOI: 10.1002/0471250953.bi1201s13

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Stormo, G. D. 2006. An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNAi Design. Current Protocols in Bioinformatics. 13:12.1:12.1.1–12.1.3.

Author Information

  1. Washington University School of Medicine, St. Louis, Missouri

Publication History

  1. Published Online: 1 MAR 2006
  2. Published Print: FEB 2006

This is not the most recent version of the article. View current version (15 OCT 2013)

Abstract

This unit briefly describes the two fundamentally different methods for predicting RNA structures. The first is to find that structure with the minimum free energy of folding, as predicted by various thermodynamic parameters related to base-pair stacking, loop lengths, and other features. If one has only a single sequence, this thermodynamic approach is the best available method. The second fundamental approach to RNA structure prediction is to use multiple, homologous sequences for which one can infer a common structure, and then try and predict a structure common to all of the sequences. Such an approach is referred to as a comparative method or phylogenetic method of RNA structure prediction.

Keywords:

  • RNA sequence and structure;
  • minimum free energy structure prediction;
  • non-coding RNA genes;
  • RNA interference;
  • comparative structure prediciton