In silico discovery of DNA regulatory sites and modules

Abstract

In this chapter we describe methods commonly applied for pattern representation and some analogies to the physical world of protein-DNA interactions. Next we present the general methodology for de novo DNA pattern discovery in a set of promoter sequences with and without prior information and we discuss some well-established algorithms. The common problems of pattern matching, i.e., the prediction of a site based on prior information are discuss along with the contribution of the evolutionary information to the pattern discovery and pattern matching algorithms. Finally, in we introduce the topic of cis-regulatory modules (CRMs) and some of the algorithms designed to find them.