Mouse Ensembl Released with FPC Based Assembly

The web site-http://mouse.ensembl.org-shows the mouse physical map assembly based around clone fingerprints (see below for credits and details), and, where retrievable sequence information. For draft and finished clones, the Ensembl automatic annotation system has been run and provides predictions of genes in these regions.

The FPC map covers an estimated 95% of the genome (as clones) and many clones have BAC-end sequences providing a integrated and useful resource for mouse mapping projects.

At the sequence level around 350MB (with redundancy), representing an estimate of about 10% of the genome is large scale sequenced clones. On this DNA we have confirmed 15,694 genes, which is an inflated number due to both redundancy at the DNA level and fragmentation between pieces of DNA. It is anticipated that there will be radical improvements to the types of data, the quality of data and its subsequence annotation over the next 3 or so months, in particular the integration of this data with the whole genome shotgun. We are releasing this current data early as a resource to the community and are working hard on many aspects, including comprehensive mouse to human linkage.

The Ensembl project is an entirely open software project supported by the Sanger Centre and the EBI, part of EMBL. The majority of its funding is from the Wellcome Trust.

Mouse Map Credits: 7,500 clone contigs assembled by fingerprinting by Marra et al. (Genome Sequence Centre, BC Cancer Research Centre, Vancouver) were extended and joined to form <600 contigs covering approximately 90% of the mouse genome. Mouse BAC end sequences from TIGR (Zhao, et al.) were used to align the mouse contigs to the human genome to accelerate the manual joining process. The synteny information was not used, however, to create joins. 6,800 markers from radiation hybrid and genetic maps of the mouse were integrated into the database to confirm contig order and orientation. For more details see Gregory et al. Further refinement of the map is in progress at the Sanger Centre and Washington University (McPherson, et al.).

Ensembl contacts:
Ewan Birney
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire, CB10 1SA
birney@ebi.ac.uk

Tim Hubbard
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire, CB10 1SA
th@sanger.ac.uk

Mouse Map contact:
Simon Gregory
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire, CB10 1SA
sgg@sanger.ac.uk