Question: predict TF binding sites from DNA sequence
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gravatar for grant.hovhannisyan
2.7 years ago by
grant.hovhannisyan1.9k 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 2.7 years ago by Bioaln340 • written 2.7 years ago by grant.hovhannisyan1.9k
1
gravatar for Bioaln
2.7 years ago by
Bioaln340
France
Bioaln340 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 2.7 years ago by Bioaln340

Thanks, will try those!

ADD REPLYlink written 2.7 years ago by grant.hovhannisyan1.9k
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