Secondary structure prediction for aligned RNA sequences

J Mol Biol. 2002 Jun 21;319(5):1059-66. doi: 10.1016/S0022-2836(02)00308-X.

Abstract

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Archaea / genetics
  • Base Sequence
  • Consensus Sequence / genetics
  • Databases, Nucleic Acid
  • Escherichia coli / genetics
  • Evolution, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Phylogeny
  • Prokaryotic Cells
  • RNA / chemistry*
  • RNA / genetics*
  • RNA Stability
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 23S / chemistry
  • RNA, Ribosomal, 23S / genetics
  • Sequence Alignment*
  • Sequence Homology, Nucleic Acid
  • Thermodynamics

Substances

  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 23S
  • RNA