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MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Alan M Moses12, Derek Y Chiang3, Daniel A Pollard1, Venky N Iyer4 and Michael B Eisen234*

Author Affiliations

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

2 Center for Integrative Genomics, University of California, Berkeley, CA 94720

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

4 Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, 1 Cyclotron Road, CA 942770, USA

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Genome Biology 2004, 5:R98  doi:10.1186/gb-2004-5-12-r98

Published: 30 November 2004

Additional files

Additional data file 1:

The fraction of binding sites that are not conserved for several different S. cerevisiae transcription factors

Format: PDF Size: 41KB Download file

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Open Data

Additional data file 2:

The conservation p-values of predicted binding sites in high-density binding site clusters in the Drosophila melanogaster genome, with the binding sites grouped according to whether the cluster has regulatory activity

Format: PDF Size: 41KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data