The JAX Synteny Browser for mouse-human comparative genomics

Mamm Genome. 2019 Dec;30(11-12):353-361. doi: 10.1007/s00335-019-09821-4. Epub 2019 Nov 27.


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: The code base is available from GitHub: and is distributed under the Creative Commons Attribution license (CC BY).

Keywords: Bioinformatics; Candidate gene analysis; Comparative genomics; Conserved synteny.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Diabetes Mellitus, Type 2 / genetics
  • Gene Ontology
  • Genomics*
  • Humans
  • Internet*
  • Mice
  • Quantitative Trait Loci / genetics
  • Synteny / genetics*