Predicting Plant Pol-II Promoter Based on Subsequence Increment of Overlap Content Diversity

Abstract

Promoter identification is the first and the most important step for understanding gene transcription regulation. In this study, one new information content feature, the subsequence increment of overlapping content diversity (IOCD), is firstly presented to describe the subsequence content of plant poll-Ⅱ promoter. The negative datasets include five different regions of Arabidopsis thaliana complete genomes, Codings, Introns, Intergenics, 5'untranslation regions (UTRs) and 3' untranslation regions (UTRs). The prediction capacity of our algorithm is tested by 10-fold cross validation test based on K- mer IOCD. The results show that the IOCD can describe the promoter sequence content well. Further, based on the interval distances between transcription start site (TSS) and translation initiation site (TIS), the method is applied to search the complete genomes of Arabidopsis thaliana and more than ten thousand probable promoters are founded.