Lawrence Berkeley National Laboratory

Reconstruction of transcriptional regulatory networks is one of the major challenges facing the bioinformatics community in view of constantly growing number of complete genomes. The comparative genomics approach has been successfully used for the analysis of the transcriptional regulation of many metabolic systems in various bacterial taxa. The key step in this approach is, given a position weight matrix, find an optimal threshold for the search of potential binding sites in genomes. Here we demonstrate that this problem is tightly bound to a problem of discovering the optimal content of regulon and suggest an approach to solve both problems simultaneously