RT Journal
A1 Couronne, Olivier
A1 Poliakov, Alexander
A1 Bray, Nicolas
A1 Ishkhanov, Tigran
A1 Ryaboy, Dmitriy
A1 Rubin, Edward
A1 Pachter, Lior
A1 Dubchak, Inna
T1 Strategies and Tools for Whole-Genome Alignments
JF Genome Research 
JO Genome Research 
YR 2003 
FD January 01 
VO 13 
IS 1 
SP 73 
OP 80 
DO 10.1101/gr.762503 
UL http://genome.cshlp.org/content/13/1/73.abstract 
AB 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.