[Chimera-users] Restricting "select by conservation" to a subset of sequences in a multiple alignment

Oliver Clarke olibclarke at gmail.com
Wed Feb 18 07:39:07 PST 2015

Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy.

I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don’t know about them!):

1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier.

2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues.

Oliver Clarke.

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