Find transcription factors that bind to inputted nucleotide sequence?

Question

[randalljellis]

Hello,

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

Thank you

Answer 1

[UnivStudent]

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.

Answer 2

[Aishwarya Kulkarni]

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

Answer 3

[Farbod]

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

Answer 4

[EagleEye]

Try MEME suite,

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

Answer 5

[randalljellis]

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

[Farbod]

I believe that we all are in the same boat !