DNA binding sites: representation and discovery

The purpose of this article is to provide a brief history of the developmen t and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be conveniently divided into two subpr oblems. The first is, given a collection of known binding sites, develop a representation of those sites that can be used to search new sequences and reliably predict where additional binding sites occur: The second is, given a set of sequences known to contain binding sites for a common factor but not knowing where the sites are, discover the location of the sites in each sequence and a representation for the specificity of the protein. Contact: stormo@ural.wustl.edu.