ArkMAP: The ArkDB map drawing application - Integrating genomic maps across species and datasources

The ability to align genetic and genomic maps within and between species and across datasources is critical for comparative genomic analyses. Whilst annotation, integration and exploration of sequence data is well supported by mainstream tools and resources, fewer tools are available for displaying maps for less well characterized species or for integrating genetic maps (linkage, QTL, radiation hybrid, cytogenetic maps etc.) with annotated reference genomes. ArkDB curates genetic mapping data for farmed and other animals. This data is available through both the ArkDB web application (where data can be browsed or displayed graphically as aligned maps) and ArkDB web services (for bulk data export in a simple XML format defined by our generic GMD schema ). To facilitate data integration we have developed ArkMAP, a desktop application that retrieves draws and aligns maps from ArkDB and Ensembl web services allowing relationships between markers on the maps to be explored within and between species. ArkMAP is freely available as a Java Webstart download from www.thearkdb.org and runs on any platform. The modular design of ArkMAP allows it to interact with any source which exports data in our GMD exchange format; alternatively, plug-in modules can be written to convert from other data formats (demonstrated by our Ensembl module). As an example, we demonstrate the use of ArkMAP to align Turkey QTL maps with regions of conserved synteny on the Ensembl annotated Chicken assembly, through Chicken linkage maps sharing Turkey markers, and ePCR maps of markers on the genome assembly.