Detection and Prediction of Alternative Splicing within Acceptor/Donor Sites in pre-mRNA of Arabidopsis thaliana

Alternative splicing is an important process in gene expression. Presently, most studies aimed at detecting alternatively spliced genes use ESTs (expressed sequence tags). However, reliance on ESTs might have some weaknesses in predicting alternative splicing. It is difficult to predict whether or not alternative splicing exists for those genes where ESTs are not available. In addition, since the EST libraries are often not clearly organized and annotated, we can pick erroneous ESTs. To address these issues and to improve the quality of detection and prediction for alternative splicing, we propose a method that primarily uses pre-mRNAs. It is achieved by a decision tree algorithm using codons, three nucleotides, as attributes for each chromosome in Arabidopsis thaliana. Each decision tree shows that alternative and normal splicing have different splicing patterns according to triplet nucleotides. Based on the patterns, alternative splicing of unlabeled genes can also be predicted.