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. 2013 Nov 22;42(Database issue):D167–D171. doi: 10.1093/nar/gkt1165

Figure 2.

Figure 2.

TF search workflow in OnTheFly. This figure describes a search for a sequence-specific transcription factor, Homeotic protein Deformed (DFD). (A) In the Entry Screen, we choose TF search. (B) A search for the term Deformed retrieves six TFs. (C) Choosing the second, DFD_DROME, leads to a detailed TF screen. This screen shows that DFD possesses a homeodomain and has two known TFBS represented by a PWM, one based on B1H data and the other based on DNase I data. (D) A homology model for this protein shows three alpha helices comprising the homeodomain shown using the MarkUs viewer. (E) The DNA sequences retrieved by DNase I are sorted according to their putative binding affinity to this protein. (F) Opening the DNaseI or B1H links shows the results of the DNA shape server (30). Each line in the graph represents the minor groove width along a different DNA sequence, which was entered as input. The graph shows that most of the sequences possess a minimum in width (narrower minor groove width in the AT part of the DNA sequence motif).