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Science 28 February 2003:
Vol. 299. no. 5611, pp. 1391 - 1394
DOI: 10.1126/science.1081331
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Reports

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Dario Boffelli,12 Jon McAuliffe,3 Dmitriy Ovcharenko,2 Keith D. Lewis,2 Ivan Ovcharenko,12 Lior Pachter,4 Edward M. Rubin12*

Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.

1 U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
2 Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
3 Department of Statistics,
4 Department of Mathematics, University of California, Berkeley, CA 94720, USA.
*   To whom correspondence should be addressed. E-mail: emrubin{at}lbl.gov

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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »
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   Abstract »    Full Text »    PDF »
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