I am from wet lab and in the very begining of my bioinformativs learning curve. Here are some rookie questions:
1. How to blast whole genome for putative transcription factor binding sites of which a JASPAR ID is available? After I am done with it, can I view it like I am viewing a peak caling BED file in USCS genome browser?
2. I have with me a BED file from published ChIP-Seq data, can I search for putative transcription factor binding site of another transcription factor I am interested in within the peaks of the BED file? Furthermore, can I search for putative binding site around the peaks in such given BED file?