A flexible model for promoter motifs
Wei-Mou Zheng1
1zheng@itp.ac.cn, Inst. Theor. Phys., Academia Sinica
Transcription factor binding sites (TFBS) can appear in different combinations on different promoters. The order of TFBSs in promoters varies, and relative distances of TFBSs in various promoters differ. Promoter is undoubtedly extremely complex. A general and flexible multi-motif model is proposed for promoter motif analysis based on dynamic programming. In the model, motifs are described with weight matrices, all possible arrangement of motifs are examined, and the total probability of training sequence set is maximized for determination of parameters. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching motifs in promoters. The algorithm is tested with plant promoters.