Using TripalMap for Genetics Research

Tripal MapViewer is a new interactive visualization tool for viewing and comparing genetic maps in CottonGen, replacing CMap. Genetic maps provided by authors in peer-reviewed papers are curated in CottonGen with standardized marker, primer and QTL names and integrated into the database with publication, contact and associated trait information. MapViewer displays complete linkage groups and allows dynamic selection and magnification of desired regions. Linkage groups from different maps and organisms can be compared and correspondences between common features are shown with hyperlinks to the individual page for each of these features, such as marker or QTL. The control panel can be used to select different reference and comparison maps, configure options for marker and QTL display patterns, and change color display of different marker types. Correspondence Matrix and Dot Plot options give a more comprehensive representation, showing where correspondences exist across multiple maps and organisms. Providing several integration points with Tripal, MapViewer offers a map overview displaying a summary graphic of all linkage groups and links to more detailed views. In this presentation we demonstrate how to use this new tool in CottonGen to answer example research questions.