AN APL-PROGRAMMED GENETIC ALGORITHM FOR THE PREDICTION OF RNA SECONDARY STRUCTURE

The possibilities of using a genetic algorithm for the prediction of R NA secondary structure were investigated. The algorithm, using the pro cedure of stepwise selection of the most fit structures (similarly to natural evolution), allows different models of fitness or driving forc es determining RNA structure to be easily introduced. This can be used for simulation of the RNA folding process and for the investigation o f possible folding pathways. Such an algorithm needs several modificat ions before it can predict RNA secondary structures. After modificatio n, a fair number of correct stems are predicted, even when using compu tationally quick, but very crude, fitness criteria such as stem length and stacking energy, including elements of tertiary structure (pseudo knots). The fact that genetic algorithm simulation includes both stem formations and stem disruption allows one to observe intermediate stru ctures that may be used in combination with phylogenetic or experiment al research.