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Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools

Weichun Huang12*, Joseph R Nevins1 and Uwe Ohler1*

Author Affiliations

1 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA

2 Current address: Department of Biology, Boston College, Chestnut Hill, MA 02467, USA

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Genome Biology 2007, 8:R225  doi:10.1186/gb-2007-8-10-r225

Published: 24 October 2007

Additional files

Additional data file 1:

Additional results of turnover simulations varying the binding site strength and GC content of the background sequences, and information on the E2F promoter data set.

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Open Data

Additional data file 2:

Additional evaluations of alignment algorithms on sequence sets simulated with a phylogenetic tree with a star topology.

Format: PDF Size: 976KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data