RFE: label residues with color-coded grid of column prevalences from associated MSA

[Elaine Meng]

Idea is to label residues with color-coded grids like we already have for deep mutational scanning (see mutationscores command) except that except for scores for each residue type, coloring is by prevalence of that residue type at that position in an associated multiple sequence alignment (MSA). This is basically the information in the associated column of a Profile Grid. Maybe it could also work for sequence alignments open in the regular Sequence Viewer as well.

My initial thought is that maybe it could be implemented as a "sequence label" commmand partially analogous to "mutationscores label" (some options would be the same, some different due to different situation). I haven't thought out the ramifications of each option, however, so depends what you guys think.

[Tom Goddard]

Here is the command syntax for the "mutationscores label" command

mutationscores label residues scoreName [mutationSet a text string] [range range] [palette a colormap] [noDataColor a color] [height a number] [offset offset] [onTop true or false]

Arguments scoreName, mutationSet, and noDataColor would not apply for sequence prevalence.

While there should be a new command for the sequence alignment case, I think I will also want the mutationscores label command to be able to handle this "score" using some special scoreName (e.g. name of the alignment). I think it could be interesting to due queries on actual DMS scores that combine sequence prevalence. For instance which mutations are gain-of-function and also observed above 20% in this deep sequence alignment?