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Evolutionary tree of *all* proteins

Georg Fuellen fuellen at techfak.uni-bielefeld.de
Tue Oct 11 05:55:51 EST 1994

In article <DRW.94Oct6155502 at taylor.mit.edu>, drw at taylor.mit.edu (Dale R. Worley) writes:
|> One can now make family trees of sequenced proteins.  In some cases,
|> the roots of these trees extend back far enough to be interesting, in
|> some cases, the divergence of the eukaryotes or before.  Since, in
|> theory, all modern proteins are descendents of a handful of primal
|> proteins, once you take the ancestries of proteins back far enough,
|> you should start to see family resemblances between proteins that
|> don't have much resemblance now, and the beginnings of the Big
|> Picture:  the family tree of ALL proteins.
|> Do we have enough data to do something like this yet, and if so, what
|> does the family tree look like?

To calculate evolutionary trees, you need to establish a distance 
between the amino acid sequences. But to get an idea of how even 2 such
sequences are related, you have to align them first, finding out where
mutations, insertions and deletions ("indels") may have taken place. 
Alignment of more than a few sequences is computationally hard, and 
even worse, the optimal alignment depends on the evolutionary tree
(you need to distinguish mutations/indels that took place close to the root 
of the tree from mutations later on; due to the noise in the data, there
may be conflicting evidence.) Indeed, some methods for constructing
evolutionary trees refine distance, tree, and alignment in a cyclic
way. Theoretically you can prove that there are no polynomial-time
approximation algorithms for the problem, if you start with nothing
but the sequences. (i.e. Generalized Tree Alignment has no poly-time
approximation scheme, see a recent preprint by Jiang, Lawler, Wang 1994.)

Comments appreciated. This topic will certainly be discussed during the 
online Biocomputing course planned to start in Spring 1995. (see 
US mirror 
(use your favorite hypertext browser (e.g. Mosaic) to view these documents.)

kindest regards,
fuellen at dali.Mathematik.Uni-Bielefeld.DE
fuellen at Techfak.Uni-Bielefeld.DE
fuellen at MIT.EDU
    Dr Stephen R Covey, The 7 Habits of Highly Effective People, Habit #3:
    Put First Things First !

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