Cis-cop: Multiobjective identification of cis-regulatory modules based on constrains

Abstract

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