#
# Performs PWM scanning with TRANSFAC and JASPAR matrices and rescores the hits according to average General Binding Preference (GBP) within the matching sites 
#

DNA = new DNA sequence dataset(DataTrack:DNA)
GBP = new Numeric dataset(DataTrack:GBP)
TRANSFAC_Public = new Motif Collection(Collection:TRANSFAC Public)
Jaspar_Core = new Motif Collection(Collection:Jaspar Core)
AllMotifs = new Motif Collection(TRANSFAC_Public,Jaspar_Core)
bgmodel = new Background Model(Model:EPD_human_3)
prompt bgmodel "Select background model"
threshold = new Numeric Variable(7.0)
prompt threshold "Select initial PWM threshold"
BindingSites = motifScanning on DNA with SimpleScanner {Motif Collection=AllMotifs,Background=bgmodel,Threshold=threshold}
BindingSites_GBPweighted=rescore BindingSites weight by average GBP