Synteny Explorer

https://wooythan.github.io/syntery-explorer/genome.html?p=EUA&c1=ponAbe&c2=musMus

Methods

linear multiple view single scale single focus segregated no abstraction linear parallel arrangement circular serial arrangement no interconnection segment sparse type

Tool

Access Format web application
Supported Files notapplicable
License open source
Tool name

Synteny Explorer
Tool Link https://wooythan.github.io/syntery-explorer/
Documentation n/a

Paper

Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution

Bryan C, Guterman G, Ma K, Lewin H, Larkin D, Kim J, et al. Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution. IEEE Trans Vis Comput Graph. 2017;23: 711–720.

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.