A comparative location database (CompLDB): map integration within and between species

Liao, Webber, Collins, Andrew, Hobbs, Matthew, Khatkar, Mehar S., Luo, Junhong and Nicholas, Frank W. (2007) A comparative location database (CompLDB): map integration within and between species. Mammalian Genome, 18, (5), 287-299. (doi:10.1007/s00335-007-9020-x).


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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/.

Item Type: Article
Digital Object Identifier (DOI): doi:10.1007/s00335-007-9020-x
ISSNs: 0938-8990 (print)
Related URLs:
Keywords: swine, research,animals, databases, computational biology, genome, cattle, chromosomes, mammalian, methods, genomics, genetic, research support, wales, australia, chromosome mapping, sheep
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Z Bibliography. Library Science. Information Resources > ZA Information resources > ZA4450 Databases
Q Science > QH Natural history > QH426 Genetics
Divisions : University Structure - Pre August 2011 > School of Medicine > Human Genetics
ePrint ID: 59990
Accepted Date and Publication Date:
May 2007Published
Date Deposited: 05 Sep 2008
Last Modified: 31 Mar 2016 12:42
URI: http://eprints.soton.ac.uk/id/eprint/59990

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