ABSTRACT
Krishna M. Roskin, Mark Diekhans, and David Haussler
Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute
University of California, Santa Cruz, CA 95064
ABSTRACT |
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We construct several score functions for use in locating unusually conserved regions in a genome-wide search of aligned DNA from two species. We test these functions on regions of the human genome aligned to the mouse genome. These score functions are derived from properties of neutrally evolving sites on the mouse and human genome, and can be adjusted to the local background rate of conservation. The aim of these functions is to try to identify regions of the human genome that are conserved by evolutionary selection, because they have an important function, rather than by chance. We use them to get a very rough estimate of the amount of DNA in the human genome that is under selection.
Keywords:neutral evolution, evolutionary models, ancestral repeat, comparative genomics, mouse-human alignments, dinucleotide dependence, mutual information, CpG effect, context-dependent base substitutions, fraction of human genome under selection
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