Question: predict TF binding sites from DNA sequence
0
gravatar for grant.hovhannisyan
17 months ago by
grant.hovhannisyan1.4k wrote:

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,

ADD COMMENTlink modified 17 months ago by Bioaln300 • written 17 months ago by grant.hovhannisyan1.4k
1
gravatar for Bioaln
17 months ago by
Bioaln300
France
Bioaln300 wrote:

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.

ADD COMMENTlink written 17 months ago by Bioaln300

Thanks, will try those!

ADD REPLYlink written 17 months ago by grant.hovhannisyan1.4k
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