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Kimura alignment

Mark Siddall mes at zoo.toronto.edu
Tue Jan 31 02:23:28 EST 1995

No offense, really, but I'm getting tired of NOT reading HSP evolution
and about green people so I'm going to try to stimulate a new thread here.

It's something that's troubled me a bit lately and think needs to be hashed
out more than I have seen it.

The problem is the weighting of alignments.  
Notwithstanding the necessary weighting of internal, leading and trailing
gaps with a particular cost.  There is also the possibility (and available
option in most multiple alignment software) for differentially 
weighting transitions and transversions.  That is, since transitions
are more likely to occur stochastically speaking, making it easier for
them to be implied in the alignment.
This is of course a simple 2 parameter Kimura model of site substitution.
My concern is as follows:
Given a multiple hit site wherein roman numerals represent taxa and letters
are bases and the following distribution of states:

Taxon   I   II   III   IV   V  VI
        A   A     G    G    T   T

And the order above implies nothing about their relationship, that is a
priori, we know nothing of relationships.
There are two possible explanations:
a) one transition and one transversion.
    for example, transformation series
      A-G-T,  or G-A-T
b) two transversions:
    for example, transformation series

The decision as to which, requires reference to some tree.  But we do not
yet have a tree, in fact, the tree is the end point of what we are 
attempting to do.
Is this not problematic for weighting transversions and transitions
in constructing multiple alignments?
Has no-one discussed this problem?

Your $0.02 please.


Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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