DETECTION OF RNA-POLYMERASE-II PROMOTERS AND POLYADENYLATION SITES INHUMAN DNA-SEQUENCE

Detection of RNA polymerase II promoters and polyadenylation sites hel ps to locate gene boundaries and can enhance accurate gene recognition and modeling in genomic DNA sequence. We describe a system which can be used to detect polyadenylation sites and thus delineate the 3' boun dary of a gene, and discuss improvements to a system first described i n Matis et al. (1995) [Matis S., Shah M., Mural R. J. & Uberbacher E. C. (1995) Proc. First Wrld Conf: Computat. Med., Public Hlth, Biotechn ol. (Wrld Sci.) (in press).], which predicts a large subset of RNA pol ymerase II promoters. The promoter system used statistical matrices an d distance information as inputs for a neural network which was traine d to provide initial promoter recognition. The output of the network w as further refined by applying rules which use the gene context inform ation predicted by GRAIL. We have reconstructed the rule-based system which uses gene context information and significantly improved the sen sitivity and selectivity of promoter detection.