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

Record type: Article

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/.

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Citation

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), pp. 287-299. (doi:10.1007/s00335-007-9020-x).

More information

Published date: May 2007
Keywords: swine, research, animals, databases, computational biology, genome, cattle, chromosomes, mammalian, methods, genomics, genetic, research support, wales, australia, chromosome mapping, sheep

Identifiers

Local EPrints ID: 59990
URI: http://eprints.soton.ac.uk/id/eprint/59990
ISSN: 0938-8990
PURE UUID: 626de859-c6b8-47ed-ad5e-210f4216979a
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 05 Sep 2008
Last modified: 17 Jul 2017 14:24

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Contributors

Author: Webber Liao
Author: Andrew Collins ORCID iD
Author: Matthew Hobbs
Author: Mehar S. Khatkar
Author: Junhong Luo
Author: Frank W. Nicholas

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