Hello there, nice Jalview people.
In the following MSA visualization, what does a dot (
.) indication in the alignment conservation annotation mean?
(I’m using Jalview 184.108.40.206)
I could not find it in the documentation, a google search, or Biostars.
[EDIT: This is an answer to a different question! See below]
The dots or hyphens represent gaps in the sequence alignment. Physically these don’t represent gaps between the residues before and after the gap in that particular protein but might indicate insertions or deletions (or even missing data depending on the source).
In Jalview gaps can be represented as spaces, dots (periods/full-stops) or hyphens.
See https://www.jalview.org/help/html/editing/index.html, https://www.jalview.org/help/html/features/preferences.html (look for “Gap Symbol”)
for info about editing/viewing gaps in Jalview.
This page: https://proteinstructures.com/sequence/sequence-alignment/ has a basic explanation of gaps in alignments too.
Hope that helps!
Hi again KaparaNewbie,
@sduce pointed out to me that I’d missed reading the words “conservation annotation” in your original question! I answered about hyphens/dots in the main alignment, but that wasn’t what you asked, so I’ve unmarked the solved flag on that post.
The dots in the conservation annotation are in fact hyphens (I agree they look like dots with the default Windows font), and they signify that that particular alignment column has more gaps than the conservation gap threshold (which is 25% of the number of sequences in the alignment (rounded down)).
Hope that answer helps better than the last one!
We should update the help page to include the information about the threshold of 3% and how this is adjustable (assuming it is)…
This is the help page https://www.jalview.org/help/html/calculations/conservation.html