Figure 1

Visualisation of putative transcription factor binding sites in BioSAVE. (A) This screenshot displays an overview of a 1.2 kb sequence that was shown to contain functional binding sites for the physically interacting androgen receptor (AR) and Ets transcription factors. Matches to the position weight matrices (displayed in (a)) of both factors were identified using the Motifscanner tool from the NestedMICA package. After selection in (b) they are being displayed as red (AR) or blue (Ets) bars above (+) or below (-) the sequence. Using the selected score threshold shown in (c), there is a wealth of putative Ets sites, as can be seen in the sequence view or motif occurrences table showing corresponding sites (d). (B) The score thresholds for the Ets factors are now adjusted to allow only the strongest putative binding sites to be shown, helping the biologist to identify biologically relevant matches to the position weight matrix.