SnpArrayDB

Crop SNParrayDB

Genetic linkage mapping enables the study of genome organisation and the association of heritable traits with regions of sequenced genomes. Comparative genetic mapping is particularly powerful as it allows translation of information between related genomes and gives an insight into genome evolution. A common tool for the storage, comparison and visualisation of genetic maps is CMap. However, current visualisation in CMap is limited to the comparison of adjacent aligned maps. To overcome this limitation and in collaboration with CMap developers, we have developed CMap3D, a tool to compare multiple genetic maps in three-dimensional space. CMap3D is based on a client/server model ensuring operability with current CMap data repositories. This tool can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps.

The software is a standalone application written in Processing and Java. Binaries are available for Windows, OSX and Linux, and require Sun Microsystems Java Runtime Environment 1.6 or later. The software is freely available for non-commercial use.

Publications

• Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. Bioinformatics 26 (2) 273-274

• Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27

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