The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. In doing so, we aim to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data.
ArkDB records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point (via the Species table or Maps menu respectively). Limited relationships between markers are recorded and displayed.
As with our previous version, all maps can be drawn using data extracted from the database "on the fly". In this version, we no longer draw maps using Java Applet technology, but provide ArkMAP a downloadable map drawing application for your desktop - that can connect directly to both ArkDB and Ensembl datasources (including EnsemblGenomes) . ArkMAP provides a more fully featured and flexible drawing interface than the Applet, and allows links between maps in ArkDB and those in the Ensembl genome projects to be visualized.
This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The ArkDB code is open source and available on request.
The ArkMAP application uses Web Services that we have implemented for ArkDB, which are available and documented at ArkDBWS, and our own JEnsembl API to retrieve chromosome gene assemblies from Ensembl and EnsemblGenomes.
We are currently developing systems to store and retrieve genetic maps for QTL mapping analyses performed on the GridQTL system. The pages to upload, browse and download maps for GridQTL are found at ArkDB:GridQTL.
The following are the 'primary' Species held in the ArkDB system:
Maps for further species may be stored in ArkDB:GridQTL.
Where possible, i.e for species with genome assemblies available at Ensembl and where primer sequence information for markers is held in ArkDB, we have mapped ArkDB markers onto the genome builds by performing ePCR. This data is presented alongside other mapping data here, as 'Sequence Maps'. However, we also provide this map data in downloadable GFF files so that the marker locations may be displayed in the Ensembl genome browser. (To display the GFF files in Ensembl follow the menu: 'Configure this page' -> tab:'Custom Data' -> menu:'Attach Remote File').