Showing papers by "John Douglas Mcpherson published in 2002"

Initial sequencing and comparative analysis of the mouse genome.

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

A physical map of the mouse genome.

Abstract: A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.

What is finished, and why does it matter.

Abstract: Our ability to acquire and analyze DNA sequence data has increased phenomenally in the past 12 years. The acquisition of both cDNA and genomic DNA sequence has exerted a major influence on the direction of biological and medical research and will continue to do so. However, the DNA sequencing field has progressed so rapidly that technical differences between various sequencing approaches have resulted in large datasets of differing quality. Although all of these datasets are valuable in their own right, they are composed of experimental data; therefore they are subject to errors, ambiguities, and incompleteness at a level related to the experimental strategy that created them. The picture is further complicated by the lack of a community-accepted nomenclature that clearly defines levels of sequence completeness. Because of the small number of people producing this resource relative to the large number using it, the nature of the data is, unfortunately, not commonly appreciated.....