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Published April 15, 2006 | public
Journal Article

Evolution at the nucleotide level: the problem of multiple whole-genome alignment

Abstract

With the genome sequences of numerous species at hand, we have the opportunity to discover how evolution has acted at each and every nucleotide in our genome. To this end, we must identify sets of nucleotides that have descended from a common ancestral nucleotide. The problem of identifying evolutionary-related nucleotides is that of sequence alignment. When the sequences under consideration are entire genomes, we have the problem of multiple whole-genome alignment. In this paper, we first state a series of definitions for homology and its subrelations between single nucleotides. Within this framework, we review the current methods available for the alignment of multiple large genomes. We then describe a subset of tools that make biological inferences from multiple whole-genome alignments.

Additional Information

© The Author 2006. Published by Oxford University Press. Received February 1, 2006; Revised and Accepted March 9, 2006. C.N.D. was supported by the NIH (HG003150). L.P. was supported by the NIH (R01-HG2362-3 and HG003150) and an NSF CAREER award (CCF-0347992). Conflict of Interest statement. None declared.

Additional details

Created:
August 19, 2023
Modified:
October 24, 2023