THE SITEGA AND PWM METHODS APPLICATION FOR TRANSCRIPTION FACTOR BINDING SITES RECOGNITION IN EPD PROMOTERS

SUMMARY Motivation: Development of methods to predict functional transcription factor binding sites (TFBSs) is very important for eukaryotic genes annotation. But the high false positive rate is a serious issue in attempts to reliably predict TFBSs. Results: We propose the combined approach to search for TFBSs. The approach compiled the SiteGA method that takes into account the interactions between different TFBS positions and position weight matrix (PWM) method. Both methods have been applied to four transcription factor (TF) types (IRF1, PPAR, SREBP and SF-1). The combined approach was tested on the set of the promoters from EPD database. The approach application allows revealing most reliable potential TFBS targets. Availability: http://wwwmgs2.bionet.nsc.ru/mgs/programs/sitega/.