Finding promoter profiles with multiobjective identification of cis-regulatory modules based on constraints

Abstract

Gene expression regulation is an intricate, dynamic phenomenon essential for all biological functions. The necessary instructions for gene expression are encoded in cis-regulatory elements that work together and interact with the RNA polymerase to confer spatial and temporal patterns of transcription. Therefore, the identification of these elements is currently an active area of research in computational analysis of regulatory sequences. However, the problem is difficult since the combinatorial interactions between the regulating factors can be very complex. Here we present a web server that identifies cis-regulatory modules given a set of transcription factor binding sites and, additionally, also RNA polymerase sites for a group of genes.