Accurate annotated assemblies of the mouse and human genomes enable a detailed comparison of the organization and evolution of the two genomes. We have completed several assemblies of both the mouse, with and without public data, and human genomes. Analysis of these assemblies suggests the mouse genome is about 10% smaller than the human genome primarily because of a difference in the content of repetitive DNA between the two genomes. More than 300,000 positions in these two genomes can be aligned with one another based on short segments of sequence similarity. These conserved segments significantly enhance the resolution of the resultant comparative maps and can be used to divide the genomes into regions of conserved-shared synteny. The genes found in such regions are highly conserved as is their relative order and orientation. Comparison of the human and mouse genome is expected to be key to deciphering the important biological information encoded in the mammalian genome. A prerequisite to comparing complex genomes such as those of mouse and human is the availability of annotated assemblies of both genomes that are comparable in quality and completeness. Since February 2001, we have assembled, annotated and delivered to our subscribers two versions of the human genome and two versions of the mouse genome. A third assembly of the human genome is being completed and will be delivered by fall of 2002. These annotated assemblies provide the starting materials for the genome-wide comparisons of the mouse and human reported here. We will begin with a description of the first Celera whole genome assembly of the mouse to provide a general basis of the quality and completeness of these data and then will report the results of a preliminary comparison between these two genomes.
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