ArkMAP

ArkMAP visualizes and aligns genetic and genomic maps to enable comparative genomic analyses and integration with Ensembl and ArkDB data sources.

Key Features:

• Data Retrieval and Integration: Retrieves genetic and genomic maps from ArkDB, Ensembl and Ensembl Genomes data sources or from local files.
• Versatile Mapping Capabilities: Uses the JEnsembl API to render maps for any Ensembl release across thousands of species and to compare different assembly versions.
• Alignment and Visualization: Aligns maps by identical or synonymous markers or by gene homology/orthology relationships from Ensembl Compara and visualizes regions of conserved synteny between species.
• Publication-quality Output: Exports publication-quality graphics of maps and map alignments.

Scientific Applications:

• Genome Evolution Studies: Investigate evolutionary relationships and genomic rearrangements by aligning genetic and genomic maps across species and assembly releases.
• Genome Assembly Projects: Support assembly validation and comparison by aligning genetic maps to reference assemblies from Ensembl.
• Gene Discovery and Identification: Facilitate gene discovery using conserved synteny and homology/orthology evidence from Ensembl Compara and mapped markers.

Methodology:

Retrieves maps from ArkDB and Ensembl/Ensembl Genomes, uses the JEnsembl API to draw maps for specified Ensembl releases, aligns maps via identical/synonymous markers or Ensembl Compara homology/orthology relationships, visualizes conserved synteny, and exports graphics.