Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Figure 2
Estimating DNA-Recognition Preferences
The DNA-recognition preferences are estimated from unaligned pairs of transcription factors and their DNA targets [2] (above). The EM algorithm [13] is used to simultaneously assess the exact binding positions of each protein–DNA pair (bottom right), and to estimate four sets of position-specific DNA-recognition preferences (bottom left).