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A parallel algorithm for estimating the secondary structure in ribonucleic acids

✍ Scribed by Y. Takefuji; C. W. Lin; K. C. Lee

Book ID
104661860
Publisher
Springer-Verlag
Year
1990
Tongue
English
Weight
292 KB
Volume
63
Category
Article
ISSN
0340-1200

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✦ Synopsis

A parallel algorithm for estimating the secondary structure of an RNA molecule is presented in this paper. The mathematical problem to compute an optimal folding based on free-energy minimization is mapped onto a graph planarization problem. In the planarization problem we want to maximize the number of edges in a plane with no two edges crossing each other. To solve a sequence of n bases, n(n -1)/2 processing elements are used in our algorithm.

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A partition function algorithm for nucleic acid secondary structure including pseudoknots
✍ Robert M. Dirks; Niles A. Pierce πŸ“‚ Article πŸ“… 2003 πŸ› John Wiley and Sons 🌐 English βš– 471 KB

## Abstract Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most phy