Review for "Aequatus: An open-source homology browser"

Completed on 17 Jul 2018 by Christophe Dessimoz.

Login to endorse this review.


Comments to author

The submission presents a web interface to compare gene structure across different closely related species. Starting with a reference gene, it provides the genomic neighbourhood and that of orthologous genes—thus enabling users to visualise local synteny (in a visualisation that is reminiscent of Genomicus). The key innovation, though, lies in a comparative display of gene structure, with an annotated gene tree on the left and a display of matching exons on the right. There are a few additional display options (tables, "sankay plots") but these are not nearly as important. Finally, there is an option to dynamically load information on the domain architecture of any gene.

The widget is well thought out and innovative, and so in general I think it will be quite useful to users. For resource developers, it is a real plus that Aequatus is available both with a full-fledged back-end integrated with Ensembl compara—which is a leading resource—while at the same time available as a javascript library only.

Inevitably I have a few points, but these should be easy to address in a revised manuscript.

Major point

- From a user standpoint, where is or will Aequetus available? For instance, will http://aequatus.earlham.ac.uk/animal_compara/ be kept up to date with the latest Ensembl release? in any case, information about the release should be provided.

- From a developer standpoint, what is the rough scaling behaviour of the tool in terms of number of genome, number of genes per family etc? What are the bottlenecks? The point is that potential developers will want to know whether the widget can scale to their resource.

Minor points

- It's not so clear what the colours mean in the gene structure view. I assume these are arbitrary colours that are nevertheless consistent across species, but I still wonder whether there is information in the fact that some exons have different intensities of the same hue, while others don't.

- Also unclear to me is the meaning of the tiny arrows between exons, as well as the very fine red, black and white lines. Consider adding a legend

Discretionary/Suggestions:

- It would be nice to have the possibility to save the current view as SVG, to facilitate inclusion in publications.