We chose a larger gap range with respect to [ 26] in order to approach the problem in a more realistic way, in which information about the binding site being sought may not be known.
After chemical or enzymatic probing, modification sites are sought.
This site soon proved unsuitable and another site was sought.
Since these binding sites were tested in vivo, evidence of sequence conservation was sought, as described.
Given transcription factors whose binding sites were enriched in transgenic or tumor gene sets, we sought upstream regulators of these TFs that may contribute to their activation or inhibition through signal transduction pathways.
Therefore, we sought TFs downstream from EGF whose binding sites were enriched in promoters of upregulated tumor genes.
Potential binding sites were elucidated by docking.
Ligand binding sites were predicted using 3DLigandSite.
Two binding sites were identified for GF.
In vertebrates, functional TF binding sites are usually clustered into a modular structure, which motivates researchers to seek cis-regulatory modules (CRMs) as the advanced predictive features for cis-regulatory element recognition [36,37].
