Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps

Area of Science:

• Bioinformatics
• Genomics
• Database Management

Background:

• Tripal is an open-source toolkit for building biological databases using the Chado schema and Drupal.
• Existing tools for genetic map visualization have limitations in interactivity and integration.

Purpose of the Study:

• To introduce Tripal MapViewer, an interactive tool for visualizing genetic map data.
• To enhance the functionality and user experience of biological websites built with Tripal.

Main Methods:

• Developed Tripal MapViewer as a replacement for Comparative Map Viewer (CMap).
• Integrated MapViewer with the Tripal API for improved data searching and seamless user experience.
• Implemented using D3.js technology for interactive visualizations.
• Enabled configuration through a control panel and administration interface for custom database queries and materialized views.

Main Results:

• Tripal MapViewer enables visualization of entire maps, linkage groups, molecular markers, quantitative trait loci (QTLs), and heritable phenotypic markers.
• Facilitates graphical comparison of maps, dot plots, and correspondence matrices.
• Improves data searching capabilities and provides a seamless user experience.

Conclusions:

• Tripal MapViewer enhances the visualization and analysis of genetic map data within biological databases.
• The tool is actively used in several major genomic databases and is under development for others.
• Offers improved performance and flexibility for data storage and retrieval in Chado.