Roslin Bioinformatics - ArkMAP

ArkMAP

ArkMAP version 2.0 is our desktop application that allows users to draw and align genetic maps. Maps of interest can be selected and downloaded from :

  • Our ArkDB database by browsing the available maps by species, analysis, chromosome etc.
  • Ensembl datasources: gene-annotated chromosome assemblies may be downloaded for any of the vertebrate species held in Ensembl or other taxa held in EnsemblGenomes.
  • Local mapping data may also be loaded and displayed by the user.

ArkMAP can be installed as an auto-updating Java WebStart application on any computer, or by using a Windows installer, a Mac Disk Image or a Java JAR file. Download options are discussed in detail, and full help documentation describing launching and using ArkMAP is available.

JEnsembl version of ArkMAP

The original version of the ArkMAP application used WebServices provided by Ensembl 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 now adapted ArkMAP to make use of the JEnsembl API for datasource access in place of the Biomart access. Our new ArkMAP application provides access to both the Ensembl Vertebrate and Ensembl Genomes (Plant, Protist, Fungi, Metazoa and Bacterial) datasources.

Example usage of ArkMAP(JEnsembl) is provided, to illustrate the exploration of gene maps downloaded from Ensembl datasources (including separate release and genome build versions of a datasource), the discovery of inter-species gene orthologies, the alignment of chromosomes exhibiting regions of conserved synteny, and the retrieval of variation data for chromosome regions. Code snips demonstrating use of the integrated JEnsembl API within ArkMAP are given.

The help documentation for ArkMAP has been updated for the refactored application, and illustrates integration of several features of the JEnsemblAPI, including version aware access to all available genome assemblies at Ensembl and EnsemblGenomes, retrieval of gene homologues, discovery of regions of conserved synteny and mapping of SNP locations.