TY  - JOUR
A1  - Kolbe, Diana
A1  - Taylor, James
A1  - Elnitski, Laura
A1  - Eswara, Pallavi
A1  - Li, Jia
A1  - Miller, Webb
A1  - Hardison, Ross
A1  - Chiaromonte, Francesca
T1  - Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
Y1  - 2004/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 700 
EP  - 707 
DO  - 10.1101/gr.1976004 
VL  - 14 
IS  - 4 
UR  - http://genome.cshlp.org/content/14/4/700.abstract 
N2  - 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. 
ER  -