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



On Fri, Sep 16, 2011 at 8:13 PM, David Marjanovic
<david.marjanovic@gmx.at> wrote:
> I see two possibilities:
>
> 1) Reconstruct the DNA sequence to exactly the level of detail you can
> guarantee, and no further. The sequence will contain lots of those extra
> symbols like R and Y. Deal with it.
>
> 2) Don't reconstruct the DNA sequence. Use the aa sequence directly for
> phylogenetic analysis. That's actually done fairly often even when the DNA
> sequence is known.

Other possibility is to analyze the DNA sequences of extant organisms
with homologous peptide sequences.

For example, the alpha-2 collagen fragment from T-rex was sequenced as:
G L P G E S G A V G P A G P I G S R

It would correspond to a DNA sequence:
GGN YTN CCN GGN GAR WSN GGN GCN GTN GGN CCN GCN GGN CCN ATH GGN WSN MGN

The correspondent chicken DNA sequence is:
GGT CTT CCT GGT GAA AGC GGT GCT GTT GGT CCT GCT GGT CCT ATT GGA AGC CGT

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.

If we had the crocodile or alligator or caiman sequence the comparison
could be improved.

[]s,

Roberto Takata