The Comparative Genome Viewer, CGV, is a visualization tool that helps
you quickly compare two genomes based on pre-computed assembly-assembly alignments.
As of April 2023, CGV contained over 120 animal, plant and fungal assemblies,
including more than 50 cross-species comparisons, and these numbers will continue to grow.
This is the CGV home page, where you select the two assemblies to compare.
We'll compare mouse genomes for two different species of the genus Mus.
To get started you can either browse the dropdown menu, or start typing the organism name.
I'll select Mus musculus in Step 1, and note the list of assemblies for the house mouse.
Once we pick the second species in Step 2, Mus pahari, the assembly fields automatically fill,
indicating that these are the only two assemblies available for this particular comparison.
Let's view the comparison. We see this ideogram view,
with the Mus pahari chromosomes laid out horizontally on top,
and the Mus musculus GRC reference chromosomes on the bottom.
The colored ribbons represent assembly-assembly alignment segments.
These are reciprocal best placed alignments by default.
We'll see how to include non-best placed alignments in a bit.
Green and purple represent opposite orientations, and you can choose,
in the "Adjust your view" menu below the graphic, to show only the forward or reverse orientation.
Notice a region of chr 1 in pahari that is aligned to chr 19 of Mus musculus.
We interpret this rearrangement to mean that part of pahari chromosome
1 is evolutionarily related to chr 19 in musculus.
Let’s zoom in further to investigate synteny between pahari chromosome 1 and musculus chr 19.
I'll click on chromosome 1 in pahari to zoom to that chr.
And then on chromosome 19 in musculus.
At this zoom level you begin to see gene annotation,
and in this case find considerable gene order synteny conservation.
To zoom you can use a mouse scroll, and click and drag to pan.
You can also select a location on the ruler to zoom.
I'll zoom in using the musculus ruler, to about 31 to 36 megabases.
These whitespaces represents gaps in the whole genome alignment. But
there may be data there that we can reveal by modifying the view.
Go to the Adjust your view menu, and include the non-best placed alignments.
In this view you do not see any changes, yet, but move the minimum alignment
size slider to a smaller size, say, 100 bases, and many more alignments appear.
Okay, I'm going to go back to the original display by using this button, "Reset to genome view."
Another way to navigate to a region of interest is to search directly for a gene name or symbol.
I'll search for gene, wnt1.
Notice that there are a few results for each of the assemblies.
Since there’s a perfect match to Wnt1,
the viewer has zoomed directly to that location on both assemblies.
What about a related gene, Wnt11?
I'll click on the row for Wint11 in the Search Results for GRCm39 to zoom to that region.
The viewer automatically zooms to the corresponding aligned region
on the other assembly, i.e. to the ortholog, if it is present.
You see synteny in this region, but there are also extra genes annotated in GRCm39, e.g. Gm33720.
When you click on an alignment ribbon, you get an information panel,
including details about the alignment, and links to the
Genome Data Viewer where you can explore different data types in separate tracks.
Let's follow the GDV link in GRCm39 to briefly show the browser view in the Genome Data Viewer.
The blue shading represents the region covered by the alignment.
Down in the Genes track you can investigate evidence for the extra annotated genes.
Many other tracks are available, including an assembly-assembly alignment track.
This is showing the same alignment data that we were viewing in CGV,
and you can zoom in to the sequence level to see differences, the red shaded bases.
Other tracks include variation data from EBI,
and you can add more tracks, or your own data, with the Tracks and User Data options.
I'll go back to the Comparative Genome Viewer to
point out some navigation and view options that I skipped over earlier.
A right-click in an aligned region gives you several options, including the ability
to download aligned FASTA for that segment, and you can create an SVG image file here,
or with the Download image button just below the viewer.
Finally, to download the full alignment data,
for example in GFF3 format, use the Download data button.
We would love to have your feedback, so please use the Feedback button at
the bottom right of the CGV Home page, where you can request that we add an assembly comparison.
CGV is developed as part of the NIH Comparative Genomics Resource (CGR),
an NLM project to establish an ecosystem to
facilitate reliable comparative genomics analyses for all eukaryotic organisms.