# Load sequences AllSequences = new Sequence Collection(File:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/motif_benchmark_sequences.txt",format=Location) # Load target binding sites Answers = new Region Dataset(File:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/answers.gff", format=GFF {Position="Genomic",Relative-offset=1,Orientation="Relative",Sort1="Position",Sort2="Type",Sort3="Score",Include module motifs=false,Skip header lines=0}) Dataset_M00621 = new Sequence Collection(List:M00621_*) Dataset_M00622 = new Sequence Collection(List:M00622_*) Dataset_M00658 = new Sequence Collection(List:M00658_*) Dataset_M00699 = new Sequence Collection(List:M00699_*) Dataset_M00733 = new Sequence Collection(List:M00733_*) Dataset_M00764 = new Sequence Collection(List:M00764_*) Dataset_M00771 = new Sequence Collection(List:M00771_*) Dataset_M00774 = new Sequence Collection(List:M00774_*) Dataset_M00797 = new Sequence Collection(List:M00797_*) Dataset_M00799 = new Sequence Collection(List:M00799_*) Dataset_M00809 = new Sequence Collection(List:M00809_*) Dataset_M00920 = new Sequence Collection(List:M00920_*) Dataset_M00929 = new Sequence Collection(List:M00929_*) Dataset_M00965 = new Sequence Collection(List:M00965_*) Dataset_M00978 = new Sequence Collection(List:M00978_*) Dataset_M00982 = new Sequence Collection(List:M00982_*) Dataset_M00983 = new Sequence Collection(List:M00983_*) Dataset_M01007 = new Sequence Collection(List:M01007_*) Dataset_M01011 = new Sequence Collection(List:M01011_*) Dataset_M01035 = new Sequence Collection(List:M01035_*) Dataset_M01036 = new Sequence Collection(List:M01036_*) Dataset_M01067 = new Sequence Collection(List:M01067_*) Dataset_not_M00621 = new Sequence Collection(!Dataset_M00621) Dataset_not_M00622 = new Sequence Collection(!Dataset_M00622) Dataset_not_M00658 = new Sequence Collection(!Dataset_M00658) Dataset_not_M00699 = new Sequence Collection(!Dataset_M00699) Dataset_not_M00733 = new Sequence Collection(!Dataset_M00733) Dataset_not_M00764 = new Sequence Collection(!Dataset_M00764) Dataset_not_M00771 = new Sequence Collection(!Dataset_M00771) Dataset_not_M00774 = new Sequence Collection(!Dataset_M00774) Dataset_not_M00797 = new Sequence Collection(!Dataset_M00797) Dataset_not_M00799 = new Sequence Collection(!Dataset_M00799) Dataset_not_M00809 = new Sequence Collection(!Dataset_M00809) Dataset_not_M00920 = new Sequence Collection(!Dataset_M00920) Dataset_not_M00929 = new Sequence Collection(!Dataset_M00929) Dataset_not_M00965 = new Sequence Collection(!Dataset_M00965) Dataset_not_M00978 = new Sequence Collection(!Dataset_M00978) Dataset_not_M00982 = new Sequence Collection(!Dataset_M00982) Dataset_not_M00983 = new Sequence Collection(!Dataset_M00983) Dataset_not_M01007 = new Sequence Collection(!Dataset_M01007) Dataset_not_M01011 = new Sequence Collection(!Dataset_M01011) Dataset_not_M01035 = new Sequence Collection(!Dataset_M01035) Dataset_not_M01036 = new Sequence Collection(!Dataset_M01036) Dataset_not_M01067 = new Sequence Collection(!Dataset_M01067) Datasets = new Sequence Partition(List:Dataset_M00621=Cluster_M00621;Dataset_M00622=Cluster_M00622;Dataset_M00658=Cluster_M00658;Dataset_M00699=Cluster_M00699;Dataset_M00733=Cluster_M00733;Dataset_M00764=Cluster_M00764;Dataset_M00771=Cluster_M00771;Dataset_M00774=Cluster_M00774;Dataset_M00797=Cluster_M00797;Dataset_M00799=Cluster_M00799;Dataset_M00809=Cluster_M00809;Dataset_M00920=Cluster_M00920;Dataset_M00929=Cluster_M00929;Dataset_M00965=Cluster_M00965;Dataset_M00978=Cluster_M00978;Dataset_M00982=Cluster_M00982;Dataset_M00983=Cluster_M00983;Dataset_M01007=Cluster_M01007;Dataset_M01011=Cluster_M01011;Dataset_M01035=Cluster_M01035;Dataset_M01036=Cluster_M01036;Dataset_M01067=Cluster_M01067) DNA = new DNA Sequence Dataset(DataTrack:DNA) CCDS = new Region Dataset(DataTrack:CCDS) Conservation = new Numeric Dataset(DataTrack:Conservation) CpG_islands = new Region Dataset(DataTrack:CpG-islands) DNaseHS_peaks = new Region Dataset(DataTrack:DNaseHS_peaks) EnsemblGenes = new Region Dataset(DataTrack:EnsemblGenes) H3K4me1 = new Region Dataset(DataTrack:H3K4me1) H3K4me3 = new Region Dataset(DataTrack:H3K4me3) RepeatMasker = new Region Dataset(DataTrack:RepeatMasker) TFBS_ChIP_Seq = new Region Dataset(DataTrack:TFBS_ChIP-Seq) Conservation_peak30 = apply Peak window of size 30 with anchor at center to Conservation PriorsGenerator_M00621 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00621) PriorsGenerator_M00622 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00622) PriorsGenerator_M00658 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00658) PriorsGenerator_M00699 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00699) PriorsGenerator_M00733 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00733) PriorsGenerator_M00764 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00764) PriorsGenerator_M00771 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00771) PriorsGenerator_M00774 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00774) PriorsGenerator_M00797 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00797) PriorsGenerator_M00799 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00799) PriorsGenerator_M00809 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00809) PriorsGenerator_M00920 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00920) PriorsGenerator_M00929 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00929) PriorsGenerator_M00965 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00965) PriorsGenerator_M00978 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00978) PriorsGenerator_M00982 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00982) PriorsGenerator_M00983 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M00983) PriorsGenerator_M01007 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M01007) PriorsGenerator_M01011 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M01011) PriorsGenerator_M01035 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M01035) PriorsGenerator_M01036 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M01036) PriorsGenerator_M01067 = new Priors Generator(Configuration:"http://tare.medisin.ntnu.no/motiflab/paper/Example1/PriorsGenerator_config.xml",trainingset.samples=4000,trainingset.subset=Dataset_not_M01067) Uniform_prior = new Numeric Dataset(1) Conservation_prior = copy Conservation Combined_prior = new Numeric Dataset(0) Priors_temp = predict with PriorsGenerator_M00621 set Combined_prior to Priors_temp in collection Dataset_M00621 Priors_temp = predict with PriorsGenerator_M00622 set Combined_prior to Priors_temp in collection Dataset_M00622 Priors_temp = predict with PriorsGenerator_M00658 set Combined_prior to Priors_temp in collection Dataset_M00658 Priors_temp = predict with PriorsGenerator_M00699 set Combined_prior to Priors_temp in collection Dataset_M00699 Priors_temp = predict with PriorsGenerator_M00733 set Combined_prior to Priors_temp in collection Dataset_M00733 Priors_temp = predict with PriorsGenerator_M00764 set Combined_prior to Priors_temp in collection Dataset_M00764 Priors_temp = predict with PriorsGenerator_M00771 set Combined_prior to Priors_temp in collection Dataset_M00771 Priors_temp = predict with PriorsGenerator_M00774 set Combined_prior to Priors_temp in collection Dataset_M00774 Priors_temp = predict with PriorsGenerator_M00797 set Combined_prior to Priors_temp in collection Dataset_M00797 Priors_temp = predict with PriorsGenerator_M00799 set Combined_prior to Priors_temp in collection Dataset_M00799 Priors_temp = predict with PriorsGenerator_M00809 set Combined_prior to Priors_temp in collection Dataset_M00809 Priors_temp = predict with PriorsGenerator_M00920 set Combined_prior to Priors_temp in collection Dataset_M00920 Priors_temp = predict with PriorsGenerator_M00929 set Combined_prior to Priors_temp in collection Dataset_M00929 Priors_temp = predict with PriorsGenerator_M00965 set Combined_prior to Priors_temp in collection Dataset_M00965 Priors_temp = predict with PriorsGenerator_M00978 set Combined_prior to Priors_temp in collection Dataset_M00978 Priors_temp = predict with PriorsGenerator_M00982 set Combined_prior to Priors_temp in collection Dataset_M00982 Priors_temp = predict with PriorsGenerator_M00983 set Combined_prior to Priors_temp in collection Dataset_M00983 Priors_temp = predict with PriorsGenerator_M01007 set Combined_prior to Priors_temp in collection Dataset_M01007 Priors_temp = predict with PriorsGenerator_M01011 set Combined_prior to Priors_temp in collection Dataset_M01011 Priors_temp = predict with PriorsGenerator_M01035 set Combined_prior to Priors_temp in collection Dataset_M01035 Priors_temp = predict with PriorsGenerator_M01036 set Combined_prior to Priors_temp in collection Dataset_M01036 Priors_temp = predict with PriorsGenerator_M01067 set Combined_prior to Priors_temp in collection Dataset_M01067 apply Sum window of size 10 with anchor at start to Combined_prior apply Sum window of size 10 with anchor at start to Conservation_prior delete Priors_temp Uniform_prior_backup = copy Uniform_prior Conservation_prior_backup = copy Conservation_prior Combined_prior_backup = copy Combined_prior normalize Uniform_prior sum to one normalize Conservation_prior from range [0,sequence.max] to range [0.02,sequence.max] normalize Conservation_prior sum to one normalize Combined_prior from range [0,sequence.max] to range [0.02,sequence.max] normalize Combined_prior sum to one BgModel = new Background Model(Model:EPD_vertebrate_3) [TFBS_prior_M00621,Mprior_M00621] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00621 [TFBS_uniform_M00621,Muniform_M00621] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00621 [TFBS_conservation_M00621,Mconservation_M00621] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00621 [TFBS_prior_M00622,Mprior_M00622] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00622 [TFBS_uniform_M00622,Muniform_M00622] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00622 [TFBS_conservation_M00622,Mconservation_M00622] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00622 [TFBS_prior_M00658,Mprior_M00658] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00658 [TFBS_uniform_M00658,Muniform_M00658] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00658 [TFBS_conservation_M00658,Mconservation_M00658] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00658 [TFBS_prior_M00699,Mprior_M00699] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00699 [TFBS_uniform_M00699,Muniform_M00699] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00699 [TFBS_conservation_M00699,Mconservation_M00699] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00699 [TFBS_prior_M00733,Mprior_M00733] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00733 [TFBS_uniform_M00733,Muniform_M00733] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00733 [TFBS_conservation_M00733,Mconservation_M00733] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00733 [TFBS_prior_M00764,Mprior_M00764] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00764 [TFBS_uniform_M00764,Muniform_M00764] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00764 [TFBS_conservation_M00764,Mconservation_M00764] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00764 [TFBS_prior_M00771,Mprior_M00771] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00771 [TFBS_uniform_M00771,Muniform_M00771] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00771 [TFBS_conservation_M00771,Mconservation_M00771] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00771 [TFBS_prior_M00774,Mprior_M00774] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00774 [TFBS_uniform_M00774,Muniform_M00774] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00774 [TFBS_conservation_M00774,Mconservation_M00774] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00774 [TFBS_prior_M00797,Mprior_M00797] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00797 [TFBS_uniform_M00797,Muniform_M00797] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00797 [TFBS_conservation_M00797,Mconservation_M00797] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00797 [TFBS_prior_M00799,Mprior_M00799] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00799 [TFBS_uniform_M00799,Muniform_M00799] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00799 [TFBS_conservation_M00799,Mconservation_M00799] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00799 [TFBS_prior_M00809,Mprior_M00809] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00809 [TFBS_uniform_M00809,Muniform_M00809] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00809 [TFBS_conservation_M00809,Mconservation_M00809] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00809 [TFBS_prior_M00920,Mprior_M00920] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00920 [TFBS_uniform_M00920,Muniform_M00920] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00920 [TFBS_conservation_M00920,Mconservation_M00920] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00920 [TFBS_prior_M00929,Mprior_M00929] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00929 [TFBS_uniform_M00929,Muniform_M00929] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00929 [TFBS_conservation_M00929,Mconservation_M00929] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00929 [TFBS_prior_M00965,Mprior_M00965] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00965 [TFBS_uniform_M00965,Muniform_M00965] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00965 [TFBS_conservation_M00965,Mconservation_M00965] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00965 [TFBS_prior_M00978,Mprior_M00978] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00978 [TFBS_uniform_M00978,Muniform_M00978] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00978 [TFBS_conservation_M00978,Mconservation_M00978] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00978 [TFBS_prior_M00982,Mprior_M00982] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00982 [TFBS_uniform_M00982,Muniform_M00982] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00982 [TFBS_conservation_M00982,Mconservation_M00982] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00982 [TFBS_prior_M00983,Mprior_M00983] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M00983 [TFBS_uniform_M00983,Muniform_M00983] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M00983 [TFBS_conservation_M00983,Mconservation_M00983] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M00983 [TFBS_prior_M01007,Mprior_M01007] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M01007 [TFBS_uniform_M01007,Muniform_M01007] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M01007 [TFBS_conservation_M01007,Mconservation_M01007] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M01007 [TFBS_prior_M01011,Mprior_M01011] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M01011 [TFBS_uniform_M01011,Muniform_M01011] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M01011 [TFBS_conservation_M01011,Mconservation_M01011] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M01011 [TFBS_prior_M01035,Mprior_M01035] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M01035 [TFBS_uniform_M01035,Muniform_M01035] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M01035 [TFBS_conservation_M01035,Mconservation_M01035] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M01035 [TFBS_prior_M01036,Mprior_M01036] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M01036 [TFBS_uniform_M01036,Muniform_M01036] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M01036 [TFBS_conservation_M01036,Mconservation_M01036] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M01036 [TFBS_prior_M01067,Mprior_M01067] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Combined_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="PRIORS" in collection Dataset_M01067 [TFBS_uniform_M01067,Muniform_M01067] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Uniform_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="UNIFORM" in collection Dataset_M01067 [TFBS_conservation_M01067,Mconservation_M01067] = motifDiscovery on DNA with MEME {Background=BgModel,Positional priors=Conservation_prior,Motif distribution="oops",Search both strands=true,Number of motifs=1,Min motif width=8,Max motif width=16,Min sites=2} motif-prefix="CONSERVATION" in collection Dataset_M01067 Predicted_sites_uniform = combine_regions TFBS_uniform_M00621,TFBS_uniform_M00622,TFBS_uniform_M00658,TFBS_uniform_M00699,TFBS_uniform_M00733,TFBS_uniform_M00764,TFBS_uniform_M00771,TFBS_uniform_M00774,TFBS_uniform_M00797,TFBS_uniform_M00799,TFBS_uniform_M00809,TFBS_uniform_M00920,TFBS_uniform_M00929,TFBS_uniform_M00965,TFBS_uniform_M00978,TFBS_uniform_M00982,TFBS_uniform_M00983,TFBS_uniform_M01007,TFBS_uniform_M01011,TFBS_uniform_M01035,TFBS_uniform_M01036,TFBS_uniform_M01067 Predicted_sites_conservation = combine_regions TFBS_conservation_M00621,TFBS_conservation_M00622,TFBS_conservation_M00658,TFBS_conservation_M00699,TFBS_conservation_M00733,TFBS_conservation_M00764,TFBS_conservation_M00771,TFBS_conservation_M00774,TFBS_conservation_M00797,TFBS_conservation_M00799,TFBS_conservation_M00809,TFBS_conservation_M00920,TFBS_conservation_M00929,TFBS_conservation_M00965,TFBS_conservation_M00978,TFBS_conservation_M00982,TFBS_conservation_M00983,TFBS_conservation_M01007,TFBS_conservation_M01011,TFBS_conservation_M01035,TFBS_conservation_M01036,TFBS_conservation_M01067 Predicted_sites_prior = combine_regions TFBS_prior_M00621,TFBS_prior_M00622,TFBS_prior_M00658,TFBS_prior_M00699,TFBS_prior_M00733,TFBS_prior_M00764,TFBS_prior_M00771,TFBS_prior_M00774,TFBS_prior_M00797,TFBS_prior_M00799,TFBS_prior_M00809,TFBS_prior_M00920,TFBS_prior_M00929,TFBS_prior_M00965,TFBS_prior_M00978,TFBS_prior_M00982,TFBS_prior_M00983,TFBS_prior_M01007,TFBS_prior_M01011,TFBS_prior_M01035,TFBS_prior_M01036,TFBS_prior_M01067 $hide(*) !order(Predicted_sites_uniform,Predicted_sites_conservation,Predicted_sites_prior) $show(Predicted_sites_uniform,Predicted_sites_conservation,Predicted_sites_prior) Benchmark_analysis = analyze benchmark {Answer=Answers,Aggregate=false} Benchmark_analysis_grouped = analyze benchmark {Answer=Answers,Groups=Datasets,Aggregate=false}