Figure 1. Description of the PRIMO algorithm.

This figure shows the calculation of a position weight matrix (PWM) score for a specific DNA sequence. The sequence window under calculation is shown at the bottom in capital letters. To the left is the PWM, which can be obtained from the Transfac or Jaspar databases. A value for each position was calculated based on the PWM value for the specific base. Underflow and the trivial zero result (if zero occurs in the PWM) were avoided as indicated.