I was wondering what is the best tool for finding transcription factor binding sites in a long genomic DNA sequence? I understand that online tools (which I have tried) such as Transfac, Promo and TFsearch are based on a database of known transcription factor binding sites. Are these databases regularly updated? Ie if you cannot find your transcription factor binding site of choice, is it reasonable to make the assumption that there just is no site in the query sequence or is it possible that your transcription factor isn't in the database?
Related to that, is there an easy to use tool that allows you to input the transcription factor binding sequence you're looking for and search for that in a genomic sequence instead?
Apologies if it's a dumb question, I'm not a bioinformatician and often the way programs and tools are set up and work are not clear.