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Cold Spring Harbor Laboratory Press, Genome Research, 4(14), p. 700-707, 2004

DOI: 10.1101/gr.1976004

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Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

Journal article published in 2004 by Diana Kolbe, James Taylor ORCID, Laura Elnitski, Pallavi Eswara, Jia Li, Webb Miller, Ross Hardison, Francesca Chiaromonte
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions.