1. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
2. Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
3. Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
4. The Institute for Genomic Research, Rockville, Maryland 20850, USA
5. Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
6. EMBL—European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
7. Department of Electrical Engineering, Washington University, St Louis, Missouri 63130, USA

Correspondence to: David R. Bentley¹ Correspondence and requests for materials should be addressed to D.R.B. (e-mail: Email: drb@sanger.ac.uk).

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.