Figure 1.

(A) The sequence of a promoter is searched for occurrences of known binding motifs for transcription factors (TFs), using a collection of position weight matrices. Matches are denoted as TF-tuples that contain the label of the TF, the positions of the match in the primary sequence, and the score provided by the corresponding matrix. Because binding sites tolerate sequence substitutions, several overlapping TF-tuples can be identified in a subset of positions. TF-tuples are graphically represented as boxes along the promoter sequence. Each TF is denoted with a different color. (B) Promoter TF-mapping of the phospholipase A1 gene (RefSeq: NM 015900, 500 nucleotides). TRANSFAC 6.3 was used as the mapping function [16]. In both cases, the TF occurrences are displayed as boxes along the promoter. In (A), the boxes are condensed in a single line. The TF-map graphical representation has been produced with the program gff2ps [27].