TFBIND INPUT

TFBIND

Please input your sequence in FASTA format, e.g.
> COMMENTS
ACATCTGCTATAAAATACGATGCAGTCACGT

or select FASTA format file
Compress result
TFBIND : Software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research.

Output format (space-separated):
Column1: Transcription factor matrix ID (from TRANSFAC R.3.4).
Column2: Transcription factor label (from TRANSFAC R.3.4). V means vertebrate.
Column3: Similarity (0.0-1.0) between a registered sequence for the transcription factor binding sites and the input sequence (at the position shown in the next column).
Column4: Position on the input sequence.
Column5: Strandness. + and - means forward and reverse strands that the transcription factor binds, respectively.
Column6: Consensus sequence (fixed) of the transcription factor binding sites. S = C or G, W = A or T, R = A or G, Y = C or T, K = G or T, M = A or C, N = any base pair.
Column7: Subsequence from the input sequence at the position - corresponding to the consensus sequence.

IMPORTANT NOTICE

  • ABOUT LICENSE

    • NO LICENSE REQUIRED.
    If you use our tool or cut-offs, could you please cite our paper:
    T.Tsunoda, and T.Takagi.
    Estimating Transcription Factor Bindability on DNA.
    BIOINFORMATICS, Vol.15, No.7/8, pp.622-630, 1999.

  • CUTOFF TABLE for TRANSFAC R.3.4

  • Contact: