Roslin Bioinformatics - ArkMAP
ArkMAP
ArkMAP is a desktop application that allows users to draw genetic maps. The maps of interest are selected and downloaded from the ArkDB database by browsing the available maps by species, analysis, chromosome etc. Gene-annotated chromosome assemblies may be downloaded via a direct link to Ensembl Biomart. Local mapping data may also be loaded and displayed by the user. This tool replicates and improves the functionality of the applet used to draw maps within the ArkDB web application.
ArkMAP is downloaded as a Java WebStart application. Full help documentation describing launching and using ArkMAP is available.
JEnsembl version of ArkMAP
The original version of the ArkMAP application, described above, uses WebServices provided by Biomart to access the gene mapping data of the Ensembl Vertebrate genome builds. Recently we have initiated the JEnsembl project to provide a Java version of the Ensembl PERL API for data access. We have adapted ArkMAP to make use of the JEnsembl API for datasource access in place of the Biomart access. Our new demo version of ArkMAP(JEnsembl) provides access to both the Ensembl Vertebrate and Ensembl Genomes (Plant, Protist, Fungi, Metazoa and Bacterial) datasources. It is currently configured to use JEnsembl data-access v1.09, together with the v1.09 configuration artifact that allows connection to the current Ensembl release 62 (EnsemblGenomes release 9).
Example usage of ArkMAP(JEnsembl) is provided, to illustrate the exploration of gene maps downloaded from Ensembl datasources, the discovery of inter-species gene orthologies and the alignment of chromosomes exhibiting regions of conserved synteny. Code snips demonstrating use of the integrated JEnsembl API within ArkMAP are given.
The original help documentation for ArkMAP is still largely applicable to the refactored application.