Mammalian Genome

, Volume 18, Issue 5, pp 287–299 | Cite as

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

  • Webber Liao
  • Andrew Collins
  • Matthew Hobbs
  • Mehar S. Khatkar
  • Junhong Luo
  • Frank W. NicholasEmail author


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


Radiation Hybrid Band File Anchor Locus Cytogenetic Band Comparative Mapping Data 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported in part by the Cooperative Research Centre for Innovative Dairy Products and by SheepGenomics. The authors thank the many researchers who have generated the data incorporated into the integrated maps. In particular, they thank Dr. Jill Maddox for much of the data on which the example of OAR18 was based. The authors also thank the referees for many helpful suggestions.

Supplementary material

335_2007_9020_MOESM1_ESM.pdf (229 kb)
ESM1 (PDF 205350 kb)


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Webber Liao
    • 1
  • Andrew Collins
    • 2
    • 3
  • Matthew Hobbs
    • 1
    • 3
  • Mehar S. Khatkar
    • 1
    • 3
  • Junhong Luo
    • 1
    • 4
  • Frank W. Nicholas
    • 1
    • 3
    • 4
    Email author
  1. 1.Reprogen, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia
  2. 2.Genetic Epidemiology and Bioinformatics Research Group, Human Genetics Division, School of MedicineUniversity of SouthamptonSouthamptonUK
  3. 3.Cooperative Research Centre for Innovative Dairy Products, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia
  4. 4.SheepGenomics, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia

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