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Proc Natl Acad Sci U S A. 1980 Nov; 77(11): 6309–6313.
PMCID: PMC350273

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


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.

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Selected References

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  • Delisi C, Crothers DM. Prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 1971 Nov;68(11):2682–2685. [PMC free article] [PubMed]
  • Tinoco I, Jr, Uhlenbeck OC, Levine MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971 Apr 9;230(5293):362–367. [PubMed]
  • Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol. 1973 Feb 5;73(4):497–511. [PubMed]
  • Tinoco I, Jr, Borer PN, Dengler B, Levin MD, Uhlenbeck OC, Crothers DM, Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. [PubMed]
  • Borer PN, Dengler B, Tinoco I, Jr, Uhlenbeck OC. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. [PubMed]
  • Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. J Mol Biol. 1973 Aug 5;78(2):301–319. [PubMed]
  • Pipas JM, McMahon JE. Method for predicting RNA secondary structure. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2017–2021. [PMC free article] [PubMed]
  • Studnicka GM, Rahn GM, Cummings IW, Salser WA. Computer method for predicting the secondary structure of single-stranded RNA. Nucleic Acids Res. 1978 Sep;5(9):3365–3387. [PMC free article] [PubMed]
  • Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sänger HL. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature. 1978 May 18;273(5659):203–208. [PubMed]
  • Jacobson AB, Spahr PF. Studies on the secondary structure of single-stranded RNA from the bacteriophage MS2. II Analysis of the RNase IV cleavage products. J Mol Biol. 1977 Sep 25;115(3):279–294. [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences


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