Grant_2011_PMID_21330290.README Last modified: 2016-04-25 Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27(7):1017-8 PMID:21330290 The motif scanner FIMO (Grant et al., 2011, Bioinformatics; PMID:21330290; http://meme.sdsc.edu) was run using the default parameters, a background of A,T: 0.31, G:C: 0.19, and the Expert Curated set of YeTFaSCo PFMs. The results were filtered by p-values at different stringencies as listed below. Data files last modified: 2012-11-06 d) SGD_PWM_predicted_binding_sites_p0.001.gff3 A GFF file of predicted motif matches by FIMO at a relaxed (p < 1e-03) p-value threshold. 127 of 129 TFs had a motif match in the genome at this threshold, except ASH1 and HAA1. e) SGD_PWM_predicted_binding_sites_p0.0001.gff3 GFF file of predicted motif matches by FIMO at a moderate/default (p < 1e-04) p-value threshold. 119 of 129 TFs had a motif match in the genome at this threshold. f) SGD_PWM_predicted_binding_sites_p0.00001.gff3 GFF file of predicted motif matches by FIMO at a stringent (p < 1e-05) p-value threshold. 81 of 129 TFs had a motif match in the genome at this threshold.