JBrowse 2: Comparative data

JBrowse 2 has the ability to display pairwise comparative data. At WormBase, we have comparative data between these species/assemblies:

C. elegans N2C. elegans Hawaiian strainC. elegans VC2010C. brenneriC. briggsaeC. inopinataC. japonicaC. remanei 

These comparisons are made with minimap2 with the option to generate CIGAR strings. The CIGAR strings allow JBrowse to show the inserts and deletions between the compared genomes.  These pre-computed comparisons can be found in a few ways from WormBase’s JBrowse.

The most straightforward way to find them is to turn on the synteny tracks when browsing the linear genome view of the assembly you are interested in.  For any assembly that has comparative genomics data, there is a track checkbox to display the orthologous regions in a related genome. For example, if you are browsing C. elegans N2, you will see a category of tracks called Synteny (usually at the bottom of the long list of tracks) that looks like this:

When I turn on the all of these tracks for N2 in the region around unc-9, it looks like this:

Not surprisingly, the other C. elegans assemblies show a large swath of similarity and the other species show less similarity. The orangish glyphs indicate matches in the same orientation as the reference sequence (N2) and the bluish tracks indicate reverse orientation matches.  To examine a given similarity, you can right- or control-click on the match region.  For example, if we do that with the l...

Source: WormBase - June 22, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news