SECONDARY STRUCTURE COMPUTER-PREDICTION OF THE POLIOVIRUS 5'-NONCODING REGION IS IMPROVED BY A GENETIC ALGORITHM

Comparison of the secondary structure of the 5' non-coding region of p oliovirus 3 RNA derived from the genetic algorithm with the model of S kinner et al. (J. Mel. Biol., 207, 379-392, 1989) demonstrates many of the confirmed structural elements. The genetic algorithm (Shapiro and Navetta, J. Supercomput., 8, 195-201, 1994) generates a population of all possible stems, then mixes, combines, and recombines these stems in multiple iterations on a massively parallel computer ultimately sel ecting a most fit structure based on its energy. The secondary structu re of the region containing the determinants of neurovirulence was bet ter predicted using the genetic algorithm, whereas the dynamic program ing algorithm (Zuker, Science, 244, 48-52, 1989) required phylogenetic comparative sequence analysis to arrive at the con ect conclusion. In addition, artificial mutations were introduced throughout this region of the genome and although rearrangements in structure may occur, man y structures persisted, suggesting that the given structures thus sele cted may have evolved to withstand isolated mutations. The genetic alg orithm-derived structure for the 5' non-coding region compares favorab ly with the biological data and functions previously described, and co ntains all of the 'persistent' structures, suggesting also that the pe rsistence factor may be an aid to validating structures.