scan for motifs in TFBS

[Melanie Fattohi]

Hi,

i have a FASTA file with promoter sequences of genes of interest. How can I use JASPAR to download motifs of transcription factors (TFs) of interest which I then scan for in the promoter sequences?

I prefer usage over the command line but I am also fine with doing this on the web interface.

Does JASPAR offer motif scanning? Or can I just download the PWM of motifs of TFs of interest and do the scanning with another tool, e.g. FIMO?

Thank you for any answer!

[Anthony Mathelier]

Hi.

Thanks for your interest in JASPAR.

If you have the genomic coordinates of your promoter sequences, you can use our TFBS extraction tool to extract TFBSs in these regions (https://jaspar.elixir.no/tfbs_extraction/). Another way I would suggest is to do the same but using our UniBind TFBSs (https://unibind.uio.no/TFBS_extraction/), which are of higher quality as they combine experimental (ChIP-seq) and computational (JASPAR PWMs) evidence of direct TF-DNA interactions.

If you only have the FASTA sequences, you can scan JASPAR motifs using the Biopython module or the Bioconductor TFBSTools package (https://jaspar.elixir.no/tools/).

Best

[Menglin Li]

Hi Anthony,

I used the TFBS extraction tool to get the score and I noticed that the score I got is P-value after scaled? However when I use the scan tool to scan the sequence with certain TFs, it always show a result of numbers that scaled 1-10. How should I intepret this score to compare with the p-value? I'm a bit confused on how the number usually ranging 1-10 comes from, I was trying to find the equations or calculations but I could not. Please let me know if I missed anything. Thank you!