TFSEARCH: DNA Transcription Factor Binding Site Prediction

Method :

Simple correlation calculation with binding site profile matrices. TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995. TFSEARCH searches highly correlated sequence fragments versus TFMATRIX transcription factor binding site profile database in 'TRANSFAC' databases developed at GBF-Braunschweig, Germany.


T. Heinemeyer, E. Wingender, I. Reuter, H. Hermjakob, A. Kel, O. Kel, E. Ignatieva, E. Ananko, O. Podkolodnaya, F. Kolpakov, N. Podkolodny, and N. Kolchanov: "Databases on Transcriptional Regulation: TRANSFAC, TRRD, and COMPEL", Nucleic Acids Res. vol.26, pp.364-370 (1998).

Yutaka Akiyama: "TFSEARCH: Searching Transcription Factor Binding Sites",

How to use :

  1. Enter any label for your sequence into top field. (optional)
  2. Paste your DNA sequence into second field. (necessary)
  3. Select a 'Classification' of matrix to be applied.
  4. Set 'Threshold score' (Optional).
    This value is the threshold score for reporting.
    Default value is 85.0 point.
  5. Push 'Clear' only if you want to reset the input form.
  6. Then, push 'Exec' button to submit your query to the server.

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