predict TF binding sites from DNA sequence

Question

[grant.hovhannisyan]

Hi Biostars,

I have two species of yeasts. I need to find which transcription factors bind to promoter region of each gene in both species and then compare TF between species. So basically I need to make a prediction of TF binding sites using promoter sequences for each gene in both species. This is possible to do using TRANSFAC, but it costs money.

Are there any alternatives to TRANSFAC? Do you recommend using Jaspar?

Would be glad to discuss this question and open for other approaches too!

Thanks in advance,

Answer 1

[Bioaln]

Have you tried any of the:

https://molbiol-tools.ca/Transcriptional_factors.htm

http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

http://jaspar.genereg.net/

JASPAR is known to be relatively OK.

[grant.hovhannisyan]

Thanks, will try those!