Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.
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.
Kolbe
Diana
D
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Taylor
James
J
Elnitski
Laura
L
Eswara
Pallavi
P
Li
Jia
J
Miller
Webb
W
Hardison
Ross
R
Chiaromonte
Francesca
F
D000199:Actins / Q000235:genetics; D000818:Animals; D022763:CCAAT-Enhancer-Binding Protein-alpha / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004247:DNA / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D006801:Humans; D051379:Mice; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data
D000199:Actins; D022763:CCAAT-Enhancer-Binding Protein-alpha; D004247:DNA