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Vol 13, Issue 1, 64-72, January 2003

LETTER

Distinguishing Regulatory DNA From Neutral Sites

Laura Elnitski1,3, Ross C. Hardison1, Jia Li2, Shan Yang1, Diana Kolbe1,3, Pallavi Eswara3, Michael J. O'Connor3, Scott Schwartz3, Webb Miller3,4 and Francesca Chiaromonte2,5,6

1Departments of Biochemistry and Molecular Biology,2 Statistics, 3Computer Science and Engineering,4 Biology, and 5Health Evaluation Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

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.

6 Corresponding author.
E-MAIL chiaro{at}stat.psu.edu; FAX (814) 863-7114.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.817703.


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