Establishing the evolutionary relationship between distantly related protein structures can yields important clues on functional relationships. For instance, resolving deep paralogous trees may help us understanding how complex molecular functions were adapted into one another through a combination of natural selection and genetic drift cycles. The evolutionary relevance of structure based comparisons has, however, recently been questioned by several high impact factor works, in which results established on simulated data suggest that some disagreements may exists between evolutionarily and structurally correct multiple sequence alignments.
In the context of this seminar, I will introduce a recently developed confidence index for multiple sequence alignments, the TCS (Transitive consistency score). I will show how this index can be used to both identify structurally correct positions in an alignment and evolutionary informative sites, thus suggesting more unity than initially thought between these two parameters. I will then introduce the structure based clustering method we recently developed to further test these hypothesis.
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