This video demonstrates recent improvements to our Multiple Sequence Alignment Viewer.
We implement changes like these based on the feedback we've received from people like you.
Thank you! And please keep the feedback coming.
For this demonstration, I'll be sending to the viewer a set of SARS-CoV-2 genome sequences
collected from our NCBI Virus resource, but the viewer can be used with other alignment
data, including BLAST results.
I've refined my virus search to a set of 434 complete SARS-CoV-2 genomes.
I'll click the top check box to select the 200 accessions on this page.
You can align up to about 500 sequences. If you want to add the next set of 200, scroll
down to select the next page, then check the top box again. I'll just align these first
200.
Click the Align button to send the sequences to the MSA viewer.
In the upper coordinate region, you see thin red lines denoting differences in the aligned
sequences.
I'll click and drag to zoom into one of these regions
The coloring menu is set to "Show differences" by default.
I'll zoom in a bit more to the sequence level, using the plus to the right of the zoom slider.
Note that a Consensus row is set by default.
And a Right-click in the consensus row provides several options.
For example, you can unset the consensus and download the consensus sequence in FASTA format.
To set a different sequence as the anchor, right-click on the desired row, and the pop-up
gives you the option to set that accession as the anchor.
I'll leave these settings unchanged for now.
You see that the default columns for this page are Sequence ID and Organism.
One major improvement is that you can now change these columns.
I'll go to the Columns settings and uncheck Organism since these are all SARS-CoV-2.
And let's say that I want to restrict the country of origin. Of course, I could have
done that in NCBI Virus, but I can now do that in the viewer by adding the Country column.
And I can also change the column widths by clicking on the current setting.
I'll also add percent identity and number of mismatches; both values are in reference
to the consensus or anchor.
To see only the samples from the USA, for example, I'll use the sorting function in
the County column.
Then I can click/shift to select all the non-USA rows; right click to show the menu and select
the option, "hide selected rows".
Similar functions are also available in the Rows dialog.
After my changes, I see in the lower right corner that Rows Shown is now 178 out of 200.
You could reverse that action with another right-click and the "Show all rows" option.
You might also want to get the best alignments at the top. Do that by sorting the percent
identity column.
Okay. Now I'd like to investigate a common polymorphism in the spike protein, known as
D614G. And let's say you know this change is at position 23403 in the consensus sequence.
Mousing over a nucleotide in the consensus shows the position,
then when you've found the position you want, move slightly up to the coordinates region
and click to set a line at that position through the alignment.
As I scroll down I begin to see a polymorphic A.
To verify an Aspartic acid at this position, I'll expand the MT520253 accession by clicking
on the downward double arrow. And sure enough, there is an Aspartic acid
residue at that position.
And a Glycine at that postion for the consensus G nucleotide.
Now let's see what happens when I set the MT520253 sequence as the anchor;
use the right-click pop-up menu to do that.
Note how the overview now shows the feature annotation, and marks the region we are viewing
in the Spike protein.
Also, the data in the percent identity and mismatch columns has updated to use the anchor
row as the reference, rather than the previous consensus row.
I'll finish up by pointing out what you can do with these sequences.
Using the Download menu, you can save the alignments in aligned FASTA format. Since
this excludes the hidden sequences, this is great for exporting only what you need for
further analysis.
The Download menu also lets you export a nice PDF or vector graphic file.
Finally, you can share this view, including your customized columns and rows, in the help
menu - click on "Link to View."
As always, we would love to have your questions and feedback. You can use the Feedback button
at the bottom of the page, or write to info@ncbi.nlm.nih.gov.