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Tool or DB to find candidate transcription factors from promoter sequences? Arabidopsis

Hi, I would like to take a promoter sequence and identify transcription factors which might bind it. Most tools and databases go the other way, identifying motifs from transcription factors.

transcription factor promoter database
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updated by Alex Reynolds Alex Reynolds • written by mcsimenc • mcsimenc

2 answers

AgrisDB

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written by JC JC

Run your promoter sequences through MEME to get conserved sequence patterns that might be TFs.

You can then use that MEME result with TOMTOM to compare against known, published TFs in the Arabidopsis database in JASPAR.

The result will tell you which TF is most similar to each of the patterns found in your promoters, if an association can be made.

The web interfaces for both tools should work fine, but you can use both on the command-line, if you want or need.

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written by Alex Reynolds Alex Reynolds

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