Frequently Asked Questions

What sequences were used in developing TFbinding?

The transcription factor (TF) binding regions in DNA were collected from the JASPAR CORE database, and the TF sequences were obtained from the UniprotKB database.

Is there any limitation on the sequence length of TF or DNA sequence?

There is no limitation on the sequence length. TFbinding takes about 20 minutes to predict TF binding sites in a DNA sequence with 20,000 nucleotides.

However, the maximum response time of the server was set to 60 minutes due to the server's resource. Therefore, DNA sequences much longer than 20,000 nucleotides may not be processed.

What characters are allowed for the DNA and TF sequences?

Only standard nucleotides and amino acids are allowed for DNA and TF sequences, respectively. Both uppercase and lowercase letters are allowed, but other characters such as -, X, or N are not allowed in the sequence.

Can I run TFbinding with a DNA sequence only without a TF sequence?

No. A pair of DNA and TF sequences should be provided to predict potential TF binding sites in the DNA sequence.
When the DNA sequence contains 15 or fewer nucleotides, TFbinding tells the user whether the input DNA sequence binds to the input TF sequence. When the DNA sequence contains more than 15 nucleotides, TFbinding finds possible TF binding regions in the DNA sequence.

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