Best method for identification of Transcription Factor Binding Sites at genome level?

Question

[xiaofeng.dong12]

Can anyone please suggest a good tool or pipeline for indication of Transcription Factor Binding Sites (such as E-box and D-box) at genome level of zebrafish?

Answer 1

[Jean-Karim Heriche]

The Bioconductor workflow generegulation demonstrates how to find putative binding sites for known TFs in a genome. There's also the match program of BioBase.