Fast algorithm for predicting the secondary structure of single-stranded RNA

Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309-13. doi: 10.1073/pnas.77.11.6309.

Abstract

A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the second matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute one structure with the lowest free energy.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Computers
  • Hydrogen Bonding
  • Nucleic Acid Conformation
  • RNA*
  • Thermodynamics

Substances

  • RNA