Using full CORE collection vs taxon-specific CORE collection

[Charlie Hale]

Hi,

My labmate and I were debating whether it's better to use taxon-specific collections for scanning versus the full eukaryotic collection of CORE motifs. We're plant biologists and are wondering whether the plant-specific database is likely to be missing any plant motifs that are deeply conserved across eukaryotes and may only be characterized in say, the vertebrate collection. Or, would you say the plant collection is sufficient in and of itself to use for TFBS prediction?

Thanks for your great work!

- Charlie

[Anthony Mathelier]

Dear Charlie.

Thanks for your interest in JASPAR and for reaching out. You could theoretically run your scan using all motifs, but interpreting the results can be more difficult as you would have to find out if a similar TF in plants could bind this motif. For an easier interpretation, you could restrict to the plant motifs; which is what I would suggest first even though you might miss some motifs.

Best