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Published on: August 15, 2019
ArkMAP: integrating genomic maps across species and data sources
1Division of Genetics and Genomics, The Roslin Institute, Royal-Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK. trevor.paterson@roslin.ed.ac.uk
BMC Bioinformatics
|August 15, 2013
Summary
This study introduces ArkMAP, a tool for visualizing and aligning genetic maps across species, aiding genome evolution studies and gene discovery. It enables comparisons between different genome versions and species, facilitating the identification of conserved synteny.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- Visualizing genetic and genomic maps aids genome evolution studies, genome assembly, and gene discovery.
- Existing tools primarily support well-characterized species, lacking support for less-characterized ones.
- Integration of genetic maps with reference genomes for cross-species comparisons is limited.
Purpose of the Study:
- To develop a versatile desktop application for drawing and aligning genetic and genomic maps.
- To enable integration of maps from diverse sources, including local files and public databases.
- To facilitate cross-species comparisons and identification of conserved genomic regions.
Main Methods:
- Developed a desktop application, ArkMAP, utilizing the JEnsembl API.
- Integrated data retrieval from ArkDB and Ensembl data sources.
- Implemented alignment methods based on shared markers and gene homology/orthology data from Ensembl Compara.
Main Results:
- ArkMAP can draw and align genetic/genomic maps for thousands of species across Ensembl versions.
- Facilitates inter-specific comparisons and comparisons between different genome assembly revisions.
- Enables visualization of conserved synteny through interactive exploration and export of publication-quality graphics.
Conclusions:
- ArkMAP allows interactive exploration of gene and variation maps for any Ensembl-curated genome.
- Users can integrate local mapping data and visualize inter-map relationships.
- The application is freely available as a Java Web Start or standalone application.
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