Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like to have access to them.
Try YEASTRACT http://www.yeastract.com/
YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references. It also includes the description of 298 specific DNA binding sites for more than a hundred characterized TFs.
This question is quite old, but I think it might be useful to mention this:
You can also look at RSAT (Regulatory Sequence Analysis Tools):
go in the Fungi portail, in "motif discovery" choose "oligo-analysis"; there you can predict putative TFBS from upstream sequences for example. It detects repeated motifs. To be more specific of Saccharomyces cerevisiae or S. pombe, select these species in the "Background model" section.