TY  - JOUR
A1  - Elnitski, Laura
A1  - Hardison, Ross C.
A1  - Li, Jia
A1  - Yang, Shan
A1  - Kolbe, Diana
A1  - Eswara, Pallavi
A1  - O'Connor, Michael J.
A1  - Schwartz, Scott
A1  - Miller, Webb
A1  - Chiaromonte, Francesca
T1  - Distinguishing Regulatory DNA From Neutral Sites
Y1  - 2003/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 64 
EP  - 72 
DO  - 10.1101/gr.817703 
VL  - 13 
IS  - 1 
UR  - http://genome.cshlp.org/content/13/1/64.abstract 
N2  - We explore several computational approaches to analyzing interspecies genomic sequence alignments, aiming to distinguish regulatory regions from neutrally evolving DNA. Human–mouse genomic alignments were collected for three sets of human regions: (1) experimentally defined gene regulatory regions, (2) well-characterized exons (coding sequences, as a positive control), and (3) interspersed repeats thought to have inserted before the human–mouse split (a good model for neutrally evolving DNA). Models that potentially could distinguish functional noncoding sequences from neutral DNA were evaluated on these three data sets, as well as bulk genome alignments. Our analyses show that discrimination based on frequencies of individual nucleotide pairs or gaps (i.e., of possible alignment columns) is only partially successful. In contrast, scoring procedures that include the alignment context, based on frequencies of short runs of alignment columns, dramatically improve separation between regulatory and neutral features. Such scoring functions should aid in the identification of putative regulatory regions throughout the human genome. 
ER  -