Binding Sites Prediction of TetR Family Repressors


This server can be used to predict DNA binding sites for transcription factors of TetR Family Repressors (TFRs). Two methods as described in the reference at the end of this page are used: a genome sequence-based method which uses ideas of phylogenetic footprinting, and a statistical energy-based method which calculates sequence energies of DNA octamers given the amino acid sequences of TFRs. Without user-provided DNA sequences, TFBSs are predicted as genome sequence fragments near the ORF of a query TFR, and as octamer DNA sequences and sequence logos representing predicted half binding sites of a query TFR. If a DNA sequence is provided by user, the given DNA sequence will be scanned for most possible TFBSs.


For detailed descripstion of the method, please read the references.

The source code and demos can be downloaded here.


* indicates required fields

i Enter correct species name if you know. For example, Escherichia coli and Streptomyces coelicolor. (optional)
*
i Enter UniProt ID if you know. For example, P0ACT4 and A0A0N0TFX2. If not known, enter 'UNKNOWN' and The system will find a UniProt ID most similar to the given sequence. (optional)
*
i Enter a text string of single letter amino acid type codes.
*
i Enter the DNA sequence (> 50bp).


Job Name:
i You can use this name to distinguish between different requests.

Your Email:

i An email will be sent to this address after finishing the job.


After submission, the calculation will be carried out on our servers. You will be navigated to a page waiting for it to finish. That page will be automatically updated with downloadable results after the calculation is finished.

If you have any problem or suggestion, please contact <longpp@mail.ustc.edu.cn>.




References:

  • Pengpeng Long, Lu Zhang, Bin Huang, Quan Chen, Haiyan Liu*, Integrating Genome Sequence and Structural Data for Statistical Learning to Predict Transcription Factor Binding Sites (to be published)