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. 1980 Nov;77(11):6309-13.
doi: 10.1073/pnas.77.11.6309.

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

R Nussinov, A B Jacobson

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

R Nussinov et al. Proc Natl Acad Sci U S A. 1980 Nov.

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.

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References

    1. Nature. 1971 Apr 9;230(5293):362-7 - PubMed
    1. Proc Natl Acad Sci U S A. 1971 Nov;68(11):2682-5 - PubMed
    1. J Mol Biol. 1973 Feb 5;73(4):497-511 - PubMed
    1. J Mol Biol. 1973 Aug 5;78(2):301-19 - PubMed
    1. Nat New Biol. 1973 Nov 14;246(150):40-1 - PubMed

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