JASPAR Q&A Forum

Hi Anthony. I have successfully downloaded the motif clustering data for vertebrates ("

Dear Maggie. Thanks for your question and your interest in JASPAR. The matrices generated from

Confirmed! The issue has been fixed on my end. Thank you for the prompt resolution and your continued

Hi. The coordinates you provide span 8 bp as they are provide in a BED file and follow the BED format

Thanks for the note. We do not have gallus gallus predictions anymore, unfortunately. But we note

Hi Moses. Could you share the exact input you provided to the tool so we can reproduce the error? On

Hi Cihan. We recommend to use the pyJASPAR python module (https://pyjaspar.readthedocs.io/en/latest/)

Hi. Do you ensure that the universe contain regions that overlap with all regions in your foreground

Hi. The TF information should be provided, isn't it in an other column? On Tuesday, June 17, 2025

Hi Menglin. If you have a BED file, you can use our TFBS extraction tool https://jaspar.elixir.no/

Thanks for your message, Menglin. I hope my other message answered your question.

Hi. As described on the JASPAR website (https://jaspar.elixir.no/genome-tracks/), the genome tracks

Hi Irene. The score number corresponds to the relative score of the PWM hit, which is obtained as (

Hello. JASPAR provides a single TF binding profile per TF per taxon. As the human and mouse Stat5 are

Thanks for your message. You must select at least one TF binding profile to run the scan on a FASTA

Thanks for raising this. These profiles directly come from CISBP, which got them from FlyFactorSurvey

Thanks for raising this issue. The FASTA file for MA0020 is indeed incorrect and should be removed as

Hi Seongjun, Thanks for bringing this up. This is because the websearch first filters the profiles

Dear Jackhao Lin. Thanks for reaching out. The 2022 release of JASPAR indeed contained a profile for

Dear Aziz, Thank you very much for your kind response. I will include the material in my manuscript.

The base ID is associated with a specific motif for a TF. JASPAR provides binding profiles per taxon,

Hi Tim. Thanks for your message, support, and query. That is a very good suggestion indeed. We will

The captcha is expected here since it is associated with a form for users to provide us support for

The Y-axis should be labeled -log10(pvalue). Thanks for raising the issue. On Monday, November 18,

Hi Romain. JASPAR is species agnostic within the same taxon. If you are interesting in mouse TFBSs,

Hi. We do not provide any background but the raw PFMs. You can transform the PFMs into PWMs with the

Dear Cen, In order to include this motif, we need TF-DNA interaction data, such as ChIP-seq or HT-

Dear JASPAR community, since i am totally new in the research of TFs, I would like to find help or

Dear colleagues and JASPAR users, We are conducting a survey to further improve JASPAR by

Thanks for the inquiry. As I previously wrote, we are not convinced that MECP2 is a DNA-binding-