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An Algorithm for RNA Pseudoknots

M. Pillsbury·J. A. Taylor·H. Orland·A. Zee
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Abstract

We further develop the large $ N $ formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to the sixth power of the length of the RNA. The algorithm itself is presented in a self-contained form for the convenience of readers interested in implementing it.

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M. Pillsbury, J. A. Taylor, H. Orland, A. Zee. 2005-09-02. An Algorithm for RNA Pseudoknots. https://arxiv.org/abs/cond-mat/0310505

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