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J Comput Biol. 2004;11(2-3):395-411.

Score functions for determining regional conservation in two-species local alignments.

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Howard Hughes Medical Institute, Baskin School of Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.


We construct several score functions for use in locating unusually conserved regions in a genomewide 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.

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