RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2004 
FD April 01 
VO 14 
IS 4 
SP 700 
OP 707 
DO 10.1101/gr.1976004 
UL http://genome.cshlp.org/content/14/4/700.abstract 
AB 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.