A comparative location database (CompLDB): map integration within and between species.
We have adapted the Location Database (LDB) map-integration strategy of Morton et al. [Ann Hum Genet 56:223-232] (1992) as above to create an integrated map for each of several species for which fully annotated genome sequences are not yet available (sheep, cattle, pig, wallaby), using all types of partial maps for that species, including cytogenetic, linkage, somatic-cell hybrid, and radiation hybrid maps. An integrated map provides not only predictions of the kilobase location of every locus, but also predicts locations (in cM) and cytogenetic band locations for every locus. In this way a comprehensive linkage map and a comprehensive cytogenetic map are created, including all loci, irrespective of whether they have ever been linkage mapped or physically mapped, respectively. High-resolution physical maps from annotated sequenced species have also been placed alongside the integrated maps. This has created a powerful tool for comparative genomics. The LDB map-integration strategy has been extended to make use of zoo-FISH comparative information. It has also been extended to enable the creation of a "virtual" map for each species not yet sequenced by using mapping data from fully sequenced species. All of the partial maps, together with the integrated map, for each species have been placed in a database called Comparative Location Database (CompLDB), which is available for querying, browsing, or download in tabular form at http://medvet.angis.org.au/ldb/.
Liao
Webber
W
Reprogen, Faculty of Veterinary Science, University of Sydney, B19, New South Wales 2006, Australia.
Collins
Andrew
A
Hobbs
Matthew
M
Khatkar
Mehar S
MS
Luo
Junhong
J
Nicholas
Frank W
FW
D000818:Animals; D002417:Cattle; D002874:Chromosome Mapping; D033481:Chromosomes, Mammalian; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016678:Genome; D013552:Swine