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Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution

Authors :
Gregory Guterman
Jaebum Kim
Jian Ma
Harris A. Lewin
Chris Bryan
Marta Farré
Kwan-Liu Ma
Denis M. Larkin
Source :
IEEE Transactions on Visualization and Computer Graphics. 23:711-720
Publication Year :
2017
Publisher :
Institute of Electrical and Electronics Engineers (IEEE), 2017.

Abstract

Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This paper presents Synteny Explorer, an interactive visualization application designed to let college students explore genome evolution of mam- malian species. The tool visualizes synteny blocks: segments of homologous DNA shared between various extant species that can be traced back or reconstructed in extinct, ancestral species. We take a karyogram-based approach to create an interactive synteny visualization, leading to a more appealing and engaging design for undergraduate-level genome evolution education. For validation, we conduct three user studies: two focused studies on color and animation design choices and a larger study that performs overall system usability testing while comparing our karyogram-based designs with two more common genome mapping representations in an educational context. While existing views communicate the same information, study participants found the interactive, karyogram- based views much easier and likable to use. We additionally discuss feedback from biology and genomics faculty, who judge Synteny Explorer’s fitness for use in classrooms.

Details

ISSN :
10772626
Volume :
23
Database :
OpenAIRE
Journal :
IEEE Transactions on Visualization and Computer Graphics
Accession number :
edsair.doi.dedup.....b28e11ae92c31e6d517b91a414fd8c67
Full Text :
https://doi.org/10.1109/tvcg.2016.2598789