Discovering cis-regulatory modules by optimizing barbecues
Discrete Applied Mathematics
Comparison of Promoter Sequences Based on Inter Motif Distance
International Journal of Software Science and Computational Intelligence
Hi-index | 3.84 |
Motivation: The process of transcription is controlled by systems of factors which bind in specific arrangements, called cis-regulatory modules (CRMs), in promoter regions. We present a discriminative learning algorithm which simultaneously learns the DNA binding site motifs as well as the logical structure and spatial aspects of CRMs. Results: Our results on yeast datasets show better predictive accuracy than a current state-of-the-art approach on the same datasets. Our results on yeast, fly and human datasets show that the inclusion of logical and spatial aspects improves the predictive accuracy of our learned models. Availability: Source code is available at http://www.cs.wisc.edu/~noto/crm Contact: noto@cs.wisc.edu