UK CropNet, Comparative analysis project page

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~ UK CropNet, Comparative analysis project page

Project coordinators

Comparative analysis

Display development

References

Comparative analysis project maintained by:

Jo Dicks (Principal Investigator)

John Innes Centre,
Norwich Research Park,
Colney, Norwich,
NR4 7UH, UK

Tel: +44 (0) 1603 452 571, Fax: +44 (0) 1603 456 844

Comparative genome analysis
The comparative analysis of plant genomes has become a key area of research within the last few years. This interest in comparative analysis is a consequence of the discovery that many plant genomes are composed of similar genomic 'building blocks'. While their intergenic DNA contents may vary, the gene order in closely related genomes is remarkably similar. This similarity in gene order should be exploited to facilitate comparative mapping within these species.

The current wealth of comparative data is an essential part of the computer resource created by the UK CropNet. The individual databases within CropNet will be linked via the comparative data and a number of facilities will be available to the users. The techniques and models involved in the linking of these comparative data are being developed in collaboration with Sam Cartinhour (Cornell University).

Display Development
Graphical displays will show the relationships between the genomes of pairs or groups of species. These displays include a Java version of the concentric ring display of Moore et al. (1995), which shows the distribution of the 'building blocks' throughout the grass genomes, each genome being drawn as a separate ring. Other displays will include the Oxford Grid display Edwards, (1991) which compares pairs of genomes. Screenshots of these displays are shown below.

An overview of other comparative mapping displays written for ACEDB databases is available. These ACEDB displays were first written for animal genomes but are now fully functional for both plant and animal data. Analytical software will be developed to maximise the utility of the data. The new software will include a tool to suggest possible locations for genes in species in which they have not been mapped, based on their map locations in closely related species.

References

Dicks, J.L. (1997) The display of comparative mapping data using ACeDB. In Genetic Mapping of Disease Genes (eds. Pawlowitski IH and Edwards JH). Academic Press. (In Press).

Edwards, J.H. (1991) The Oxford Grid. Ann. Hum. Genet. 55:17-31

Gale, M.D. and Devos, K.M. (1998) Plant Comparative Genetics after 10 Years. Science 282:656-659

Moore, G., Devos, K.M., Wang, Z. and Gale, M.D. (1995) Grasses, line up and form a circle. Current Biology 5:737-739

~ Links

FTP site
Download our databases from the CropNet FTP site

ACEDB
ACEDB site at Sanger Centre

NASC
Nottingham Arabidopsis Stock Centre

SCRI
Scottish Crop Research Institute

John Innes Centre
Research centre for Plant Science. Also home to BrassicaDB, MilletGenes and ComapDB

IGER
Institute of Grassland and Environmental Research

Garnet
Genomic Arabidopsis Resource Network

Page last modified: Friday, 19-Oct-2001 16:50:36 BST

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