UK CropNet: AN INFORMATION RESOURCE FOR PLANT COMPARATIVE GENOMICS

¹ NASC, Division of Plant Science (UP), University of Nottingham, Nottingham, NG7 2RD, UK

² Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

³ USDA-ARS and Department of Plant Breeding, Cornell University, Ithaca, NY 14853 USA

⁴ John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

⁵ Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK

The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 as part of the BBSRC's Plant and Animal Genome Analysis special initiative. In the past year we have made significant progress, both in terms of delivering data through easily accessible databases and in the development of new software tools and displays that allow the user to gain added value from their data.
In September 1998, BrassicaDB went online, joining AGR, BarleyDB, FoggDB and MilletGenes as public UK CropNet databases. It contains genetic maps, a complete set of published B. napus sequences and an extensive bibliography. Future initiatives include collaboration with the USDA-funded CabbagePatch database and the addition of B. oleracea data. A further new development is SPUDBase, a database for potato that will go online in the near future.
We have added to our series of JavaBean displays the new CPG Map and an interactive WebAce compliant Java Bean called the Pairwise Comparative Map. The latter allows comparison of many types of chromosomal maps, including linkage and physical maps within and between species. The UK CropNet's Recombinant Viewer has been adapted and a new coloured text viewer has been developed to aid in the data interpretation of the Map_population class within AGR. Work has begun on the visualisation of graphical genotypes for both diversity analysis and for the identification of genotyping errors in mapping populations within BarleyDB. Other software tools include a WWW environment for the efficient processing of EST and SSR sequence data.
The key focus of the UK CropNet project is the development, management and distribution of information, centred on a core system of comparative genomic links. We are developing a CORBA system to facilitate complex comparative genome analysis. Our prototype front-end uses a JavaBean and the InfoBus to extract information from the individual UK CropNet databases, to collate the results of these cross-species queries and to channel them to the UK CropNet graphical displays.
The new AcePerl module (Lincoln Stein) has led to many new developments. A new prototype CORBA interface to ACEDB (CITA) allows connection to a variety of ACEDB databases independent of their underlying model schemata. AcePerl has allowed greater integration of maps, sequence and mutant information within AGR. In particular, the RI map has been augmented by fixing sequencing template clones to the nearest RI marker and sequence contigs are also anchored to the map.