The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research.
While the new genome browser (JBrowse) implemented at WormBase has several advantages, like faster browsing and a faceted track selector, it does lack a few features from the venerable GBrowse instance that has been at WormBase for many years. While we and the JBrowse developers are working on addressing those minor shortcomings, this article is about how to circumvent one of those issues now.
JBrowse lacks the ability to make a high resolution image like GBrowse. While taking a screenshot can sometimes result in an acceptable image (for example, Macs with a retina display work pretty well), the result is not always suitable for publication or putting on a poster. The method described here still does not allow for making an SVG image, but it does allow for higher quality PNG images than just taking a screenshot and also allows for the creation of a PDF document with the image in it. Unfortunately, this method requires downloading a tool where we must edit one of the source files and then execute it on the command line. While this is a little bit of a hassle, once it is set up, creating screenshots is quite easy.
This is an example of attaching an external annotation file to the ParaSite browser.
We will use BigWig as format, as the size of WIG files is limited to 5MB, which would only cover parts of the Trichinella spiralis genome (as the format contains a score for each base pair).
Disclaimer: this data is just an example and should not be used for a in depth study of conservation
We will start at the ParaSite main page and choose Trichinella spirlalis
From there we should end up on a species specific page, where we can search for, as example, EFV62134 (which is a INSDC identifier of an T.spiralis gene)
from there we will pick “Trichinella spiralis” as genome, “BigWig” as file format and put “http://www.ebi.ac.uk/~mh6/tspiralis.phylop.wib” into the URL (which you potentially need to change to wherever you host it from).
It is also possible to change the display of the track by clicking on the gear shaped icon next to it.
If you want to see all the data that you were used to seeing on the gene page, remember to open the related widgets on the left sidebar. For example, if you want to see all the alleles/variations of a gene, remember to click on the ‘Genetics’ widget. Once you do this, this preference is remembered.