Transcription factors are crucial for sequence‐specific control of transcriptional regulation. Classically, the computational prediction of transcription factor binding sites (TFBS) depends on position weight matrices (PWMs) (Wingender et al., 2001), which give weights to each nucleotide at each position. These models strongly suggest that each nucleotide participates independently in the corresponding DNA–protein interaction and does not account for flexible length motifs.
To predict the transcription binding site by using the TRANSFAC and MATCH tools
TRANSFAC is a database of TRANScription regulatory FACtors, and is maintained at GBF Braunschweig (Wingender et al., 2000). It combines the data regarding transcription factors, their DNA binding sites, sources of the factors and systematic classification of transcription factors. All the experimental results are accessible mainly through the FACTORS and the SITES table (Frech et al., 1997).
The data regarding binding proteins and the DNA sequences that are recognized by ...