Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm

Motivation Using the genetic algorithm (GA) for RNA folding on a massively parallel supercomputer, MasPar MP-2 with 16384 processors, we successfully predicted the existence of H-type pseudoknots in several sequences Results The GA is applied to folding the tRNA-like 3′ end of turnip yellow mosaic virus (TYMV) RNA sequence with 82 nucleotides, the 3′ UTRs of satellite tobacco necrosis virus (STNV)-2 RNA sequence with 619 nucleotides and STNV-1 RNA sequence with 622 nucleotides, and the bacteriophage T2, T4 and T6 gene 32 mRNA sequences with 946, 1340 and 946 nucleotides, respectively. The GA's results match the phylogenetically supported tertiary structures of these sequences. Availability Available on request from B.A.Shapiro Contact E-mail: bshapiro@ncifcrf.gov