PMID: 6161375Nov 1, 1980Paper

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

Proceedings of the National Academy of Sciences of the United States of America
R Nussinov, A B Jacobson

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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Citations

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Nov 26, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Walter Fontana
Jan 1, 1984·Journal of Mathematical Biology·R Nussinov
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Sep 17, 2009·Theory in Biosciences = Theorie in Den Biowissenschaften·Markus E Nebel, Anika Scheid
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