I have got a sequence of my human promoter of interest-reporter (pGL4) vector of 3Kbp. The promoter sequence is in capital letters (representing the nucleotides) and the reporter vector sequence is in small letter within the same sequence. Now I want to find out the transcription factor binding site. How can I find it?
Is there any software that may help to finding the possible binding sites?
Take the promoter sequence and scan it with some tools of the MEME suite to either find enriched TF motifs (AME) or scan for known motifs (FIMO). Good luck.
You may scan in silico for binding site matches e.g. with MatInspector.
You should know what the genomic location of your promoter sequence is and you can look for overlaps from ENCODE ChIP data.
I agree with Fabrice. When I need to search for a transcription factor binding site (with known consensus) within a promoter I start by using FIMO. FIMO is a part of the MEME suite - I've attached the link. Best of luck!
http://meme-suite.org/doc/fimo.html
Thank you all. But I am not clear yet. I used PROMO to find out possible TF binding sites; but my known promoter sequence is of -3kb. Therefore, I want to find the upstream TF binding sequences i.e. in negative form like -1kb, -800b like these from the starting site of transcription. So, how can you help me please?
Regards
that can be done easily through your fasta file that contains the -3kb sequence including your motifs
then, you want to know the upstream position for your predicted motif,
so let assume the position is x
length of your motif is y
length of fragment starting from after your motif and ending with the 3000th nucleotide is z
then,
x = - (y + z)
that can be done manually with any text editor rather than a sequence editor.
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