Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
             

THE APPLICATION OF ACEDB TO COMPARATIVE MAPPING IN ANIMALS AND PLANTS

¹ John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

² Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK

The original Oxford Grid, described in Mendelian Inheritance in Man and in the comparative mapping section of http://www2.bioch.ox.ac.uk/~jhe/, consists of a square, with the two axes defining different organisms, divided into rectangles with sides proportional to chromosome lengths of the two species. Recent advances in the ACEDB database management and analysis software (http://www.acedb.org/) allow the position of loci to be defined by coordinates when, if the positions and order are correctly inferred, they should show arrays of points in a diagonal without any disruption, or 'kinks', in the slope. This should be fairly close to a diagonal, either top left to bottom right, or vice versa, depending on the relative orientation. These points will be overlaid by a transparent rectangle defined by in situ mapping, within which all points should lie. Multillelic loci make it efficient to ignore the limited information provided by the mating of identical heterozygotes and produce independent paternal and maternal gametic maps, providing a check on inferences of order, a difficult problem so far inadequately resolved, and, if order correct, a direct representation of differing genetic lengths. The paternal and maternal gametes would be represented on the axes. Any 'outlier' can be defined by clicking, often with immediate access to a relevant external database such as OMIM, OMIA, LDB (the location data base) and MDB (mouse data base). Any pair of species with sufficient data can be invoked. The input files are very simple, and easily extended or modified by any text editor. The database is formed within the computer using only relevant input files. Here we will show examples of the ACEDB Oxford Grid for various animal and plant species. Versions of ACEDB are available for PCs, Macs, LINUX and UNIX (ftp.sanger.ac.uk/pub/acedb). These extensions are at present limited to the UNIX and LINUX versions and will be available at the conference. In future, it is hoped they will form part of the core ACEDB distribution.