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An APL-programmed genetic algorithm for the prediction of RNA secondary structure

✍ Scribed by F.H.D. Van Batenburg; A.P. Gultyaev; C.W.A. Pleij

Publisher: Elsevier Science
Year: 1995
Tongue: English
Weight: 827 KB
Volume: 174
Category: Article
ISSN: 0022-5193
DOI: 10.1006/jtbi.1995.0098

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✦ Synopsis

The possibilities of using a genetic algorithm for the prediction of RNA secondary structure were investigated. The algorithm, using the procedure of stepwise selection of the most fit structures (similarly to natural evolution), allows different models of fitness or driving forces determining RNA structure to be easily introduced. This can be used for simulation of the RNA folding process and for the investigation of possible folding pathways. Such an algorithm needs several modifications before it can predict RNA secondary structures. After modification, a fair number of correct stems are predicted, even when using computationally quick, but very crude, fitness criteria such as stem length and stacking energy, including elements of tertiary structure (pseudoknots). The fact that genetic algorithm simulation includes both stem formations and stem disruption allows one to observe intermediate structures that may be used in combination with phylogenetic or experimental research.

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