Figure 3

Transcription factor binding site (TFBS) motif model. Sequences known to be bound by a specific transcription factor (for example, SPI1) are aligned. A position frequency matrix (PFM) is generated by counting the number of times each type of nucleotide occurs at each position of the alignment. The PFM is then converted to a log-scale position-specific scoring matrix (PSSM). The score of any DNA sequence window, having the same length as the matrix, is calculated by summing the corresponding nucleotide values from the PSSM. The PFM may also be represented as a binding site logo, depicting the nucleotide properties of the TFBSs.