7.3 years ago by
Washington University, St Louis, USA
This very much depends on what you are trying to accomplish.
TRANSFAC and JASPAR are databases of transcription factor binding models. Using experimental techniques like SELEX and now increasingly ChIP-Seq we can identify the kinds of sequences that a particular transcription factor (TF) has affinity for. This affinity is typically represented with something like a position weight matrix (PWM) or position-specific scoring matrix (PSSM). Those models can be used to scan a genome for "putative TF binding sites" that have a high similarity to the model. Whether those sites are actually bound by a TF and play a functional role in transcription and under what conditions must still be determined experimentally be traditional molecular techniques like promoter bashing, reporter gene assays, ChIP experiments, etc.
Databases like ORegAnno and PAZAR have attempted to collect and curate individual experimentally proven TFBSs from the literature and sets from ChIP-Seq and other genome-wide experiments. Technologies like ChIP-Seq can give us a genome-wide profile of all the binding sites for a particular transcription factor under a specific condition. Many of these TF binding sites (TFBSs) are being deposited into species-specific databases (FlyBase, SGD, etc) and as tracks in the UCSC browser. In particular, see efforts by ENCODE. A good starting point would be to look through the tracks under 'Regulation' in the UCSC Genome Browser for your species of interest.