Document Type

Article

Publication Date

12-1-2019

Keywords

JMG, JGM

JAX Source

Mamm Genome 2019 Dec; 30(11-12):353-361

Volume

30

Issue

11-12

First Page

353

Last Page

361

ISSN

1432-1777

PMID

31776723

DOI

https://doi.org/10.1007/s00335-019-09821-4

Grant

CA034196,CA089713,HG007053,HG000330

Abstract

Visualizing regions of conserved synteny between two genomes is supported by numerous software applications. However, none of the current applications allow researchers to select genome features to display or highlight in blocks of synteny based on the annotated biological properties of the features (e.g., type, function, and/or phenotype association). To address this usability gap, we developed an interactive web-based conserved synteny browser, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genome according to the biological attributes of the features. Although the current implementation for the browser is limited to the reference genomes for the laboratory mouse and human, the software platform is intentionally genome agnostic. The JAX Synteny Browser software can be deployed for any two genomes where genome coordinates for syntenic blocks are defined and for which biological attributes of the features in one or both genomes are available in widely used standard bioinformatics file formats. The JAX Synteny Browser is available at: http://syntenybrowser.jax.org/. The code base is available from GitHub: https://github.com/TheJacksonLaboratory/syntenybrowser and is distributed under the Creative Commons Attribution license (CC BY).

Comments

The authors gratefully acknowledge the contributions of Keith Sheppard (The Jackson Laboratory) and Mei Xiao (Novartis Institutes for BioMedical Research) on an early version of the JAX Synteny Browser software. We also thank the numerous beta testers of the Browser for their helpful feedback and suggestions for improvements to the interfaces.

This open access article is licensed under a Creative Commons Attribution 4.0 International License

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