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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)

On Sat, Sep 17, 2011 at 1:20 AM, Tim Williams <tijawi@gmail.com> wrote:
> Sadly no, this is simply not correct.  We can't use the chicken's DNA
> sequence to fill in the blanks in the inferred _Tyrannosaurus rex_ DNA
> sequence.  It cannot be assumed that _T. rex_ has the exact same codon
> for each amino acid residue as the chicken.

You simply cut the part of the email message in which I actually
showed how to make comparisons. So I will reproduce it:
"That comparison allow us to have some improved knowledge about T-rex's
DNA sequence. For example, the second codon first position in T-rex
most probably was a C too (and not a T). Of course we cannot rule out
the possibility of point mutation (either from T to C in chicken or C
toT in T-rex).

The sixth codon is more dramatic. The S aa could be coded by a TCN
codon or by a AGY codon. In the chicken it is AGC codon. It would take
at least two point mutations to convert a TCN into AGY and vice-versa.
So, most probably T-rex had a AGY codon in that position."

And there is no place in which I said that the T.rex has the exact
same codon for each aa residue as the chicken.

>  As David says, the best we can do is use the degenerate sequence (i.e., with 
> those
> "extra symbols" reflecting an unknown base position), because we cannot know,
> and will probably never know, what the DNA sequence is for _T. rex_.

And as I've showed, we could do better than this by comparative analysis.

> BTW, the sequence you provide for _T. rex_ alpha-2 collagen (above) is
> exactly the same as that for the chicken (GLPGESGAVGPAGPIGSR).  It is
> not one of the six _T. rex_ collagen sequences deposited by Asara et
> al. (2007) in GenBank.


> Of course, all this assumes that the peptide sequence actually comes
> from _T. rex_.

Yes of course. It is just the proof of concept.

>> If we had the crocodile or alligator or caiman sequence the comparison
>> could be improved.
> No, it would make no difference at all.

It would make difference, since it could help in philogenetic bracketing.


Roberto Takata