A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison

Nucleic Acids Res. 1991 May 25;19(10):2707-14. doi: 10.1093/nar/19.10.2707.

Abstract

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Base Sequence
  • Evaluation Studies as Topic
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny*
  • RNA / chemistry*
  • RNA, Ribosomal, 16S / chemistry
  • Thermodynamics

Substances

  • RNA, Ribosomal, 16S
  • RNA