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Vol 13, Issue 1, 73-80, January 2003

LETTER

Strategies and Tools for Whole-Genome Alignments

Olivier Couronne1,3, Alexander Poliakov1, Nicolas Bray1, Tigran Ishkhanov1, Dmitriy Ryaboy1, Edward Rubin1, Lior Pachter2,3 and Inna Dubchak1

1Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 2Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA

The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for the subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of the human genome with the Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards the end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between the human and mouse genomes, some of which have not been identified by other methods.

3 Corresponding author.

E-MAIL ocouronne{at}lbl.gov; FAX (510) 486-5717.
E-MAIL lpachter{at}math.berkeley.edu.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.762503.


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