## 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.

Original language | English |
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Pages (from-to) | 6309-6313 |

Number of pages | 5 |

Journal | Proceedings of the National Academy of Sciences of the United States of America |

Volume | 77 |

Issue number | 11 |

DOIs | |

State | Published - Nov 1980 |