Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments

Daniel A Pollard¹ , Alan M Moses¹ , Venky N Iyer² and Michael B Eisen^1,2,3,4

¹Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA

²Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA

³Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, CA 94720, USA

⁴Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA