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rcsb / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry
GNU Lesser General Public License v2.1
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Detect duplication events from phylogenetic tree of symmetric repeats #74

Open lafita opened 8 years ago

lafita commented 8 years ago

The goal is to find reliable duplication events in the phylogenetic trees of symmetric repeats, once they have been identified with CE-Symm. The automatic detection of evolutionary events will allow to find interesting cases, ideally unknown before, and systematically analyze new structures.

The method, given the symmetry group and the phylogenetic tree of the repeats, determines which is the most probable succession of events in evolution (if there is enough evidence from the branch lengths).

A possible implementation is to follow the nodes of the tree and check for consistency between the symmetry relations of the repeats and the closest repeats (leaves) in the tree. In case they are consistent, the significance of the tree needs to be checked, because the branch lengths than separate duplication events need to be significant

sbliven commented 8 years ago

I think the key will be having reliable statistics on the accuracy of the topology. I'm guessing that most cases will not have sufficient significance to draw conclusions (which is OK if we're accurate on the significant cases)