Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This project presents Synteny Explorer, based on a collaboration with the UC Davis genomics department. It is a new interactive visualization application designed for introductory teaching of the genomic rearrangments that happen during species evolution.
Specifically, the tool focuses on visualizing synteny blocks: segments of homologous DNA shared between extant species that can be traced back or reconstructed in extinct, ancestral species. By using a karyogram-based approach to create an interactive synteny visualizations, we create a more appealing and engaging design for undergraduate-level genome evolution education.
The initial work for this project was presented at the IEEE Vis 2016 conference (SciVis tract) in Baltimore, MD, in October 2016.
Paper:
Bryan, Chris, Gregory Guterman, Kwan-Liu Ma, Harris Lewin, Denis Larkin, Jaebum Kim, Jian Ma, and Marta Farre.
“Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution.” IEEE transactions on visualization and computer graphics 23, no. 1 (2017): 711-720. pdf
Video:
Introduction
Personnel:
Computer Science, UC Davis
Computer Science, UC Davis
Computer Science, UC Davis
Genomics, UC Davis
