International Mammalian Genome Society

The 15th International Mouse Genome Conference (2001)


POSTER 191 -  USE OF WEB-BASED DATABASES TO REFINE THE MOUSE MAP

Dr Rosemary Elliott
Roswell Park Cancer Inst.
Elm St. at Carlton St.    
Buffalo, NY 14263
USA

The Chromosome Committee maps are a good place to start to refine the maps of mouse chromosomes or chromosomal regions.  The maps can be downloaded as EXCEL files from MGI by opening Chr Com in the banner at the top of the page.  MGI can be searched for additional mapped markers that can be incorporated directly into the maps.  ESTs from the RH data files of The Jackson Laboratory Mapping Panels may be incorporated into the maps by interpolation using MIT markers and mapped genes for comparison.  MOUSEBLAST can be used to identify genes.  Sequence from genes, ESTs and SSTs can be BLASTed against the NCBI nr and htgs databases to obtain information on mouse and human BACs carrying these loci.  This generates a useful collection of mapped BACs that help to map other loci.  This has been done for Chrs 6, 8, 12, 19 and X.  Map order can then be refined to utilize the fact that loci on the same BAC are very close.  Syntenic markers can often be placed on the map using this approach.  Overlapping BACs are also helpful in refining the map.  Human map data from the Human Genome Project Working Draft at UCSC can be used to add new markers with sequence that can be identified with mapped BACs and thus integrated into the map.  In some map regions the Celera database is extremely helpful in adding genes and other loci to the map.


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