Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

Stefan M. Hebsgaard, Peter G. Korning, Niels Tolstrup, Jacob Engelbrecht, Pierre Rouzé 1 and Søren Brunak

Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, DK-2800 Lyngby , Denmark and
1 Laboratoire Associé de l'INRA, V.I.B., University of Gent, K. L. Ledeganckstraat 35, B-9000 Gent , Belgium

Nucleic Acids Research, 24(17):3439-3452 (Sept 2, 1996)

Abstract

Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana . A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction. An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5 ' end of exons. The method presented here has been compared with three other approaches, GeneFinder, GeneMark and Grail. Overall the method presented here is an order of magnitude better. We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html.