Question: Find transcription factors that bind to inputted nucleotide sequence?
2
gravatar for randalljellis
3.8 years ago by
randalljellis80 wrote:

Hello,

Is there a tool where you input a nucleotide sequence, and the tool outputs which transcription factors bind to that sequence?

Thank you

transcription factor • 1.2k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by randalljellis80
3
gravatar for UnivStudent
3.8 years ago by
UnivStudent380
Canada
UnivStudent380 wrote:

I'd recommend the "Scan single sequences for TF binding" tool in CIS-BP using TFs from whatever species you're interested in, or TFs that you're interested in and added to your cart. Alternatively, FIMO is a popular tool from the MEME suite that can be used online, or run on the command line.

ADD COMMENTlink written 3.8 years ago by UnivStudent380
2
gravatar for Aishwarya Kulkarni
3.8 years ago by
United States
Aishwarya Kulkarni80 wrote:

HOMER is the best tool I have used so far in terms of ease and good documentation , let me know if you need any help with it : http://homer.salk.edu/homer/index.html

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Aishwarya Kulkarni80
2
gravatar for Farbod
3.8 years ago by
Farbod3.3k
Toronto
Farbod3.3k wrote:

Dear randalljellis, Hi.

"Catalog of Inferred Sequence Binding Preferences" would be a choice as it Scan a DNA sequence for potential binding sites and can Compare a given motif to all TFs in the database.

http://cisbp.ccbr.utoronto.ca/TFTools.php

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Farbod3.3k
1
gravatar for EagleEye
3.8 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

Try MEME suite,

http://meme-suite.org/index.html

ADD COMMENTlink written 3.8 years ago by EagleEye6.6k
1
gravatar for randalljellis
3.8 years ago by
randalljellis80 wrote:

Thank you all so much! I don't know what I would do without this community. I upvoted all of you :)

ADD COMMENTlink written 3.8 years ago by randalljellis80
1

I believe that we all are in the same boat !

ADD REPLYlink written 3.8 years ago by Farbod3.3k
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