We poor people in Europe receive journals like SCIENCE with a
certain delay. Having read a posting about the Gonnet et al. paper, I
rushed onto the last issue to read it.
It gave me goose flesh. And I'm reassured to see that D. Davison
thinks the same.
- in the summary: " Definitive mutation matrices ....". Later: "The
parameters provide definitive answers ..." !! How can a scientist
write that he got a *definitive* answer to anything ?
- what is a "liberal target score" ??
- "mutation matrices ... differ, depending on whether they were derived
from protein pairs that are distantly homologous or from protein pairs
that are closely homologous". What a discovery !!
- how can anyone align confidently protein sequences that are "distantly
homologous" and use the results to build a matrix ?
- what are "distantly homologous" proteins ? Two proteins that get a low
score when aligned ? I bet that this is the case between *any* pair of
sequences. GAP or BESTFIT, for example, will always return something..
Or, maybe, two proteins whose score is below a "liberal target score" ?
- what is the influence of the enormous redundancy found in protein
databanks (hundreds of cytochromes, thousands of histones, zillions of
globulins, ...)
- the explanation for the -3/2 power concerning the probability of a gap is
a joke ? Seems like an insertion is made up by synthetizing an
oligopeptide whose ends must lie close together, then open the protein
where the insertion must take place, and then insert the oligopeptide ...
Well, I prefer to stop here. May I draw your attention on the paper
by Jones, Taylor and Thornton in the last CABIOS issue ? Their aim was also
to build an updated Dayhoff matrix. They did it, with the difference that
their procedure is crystal clear. And that, by necessity, their matrix was
not built with "distantly homologous proteins".
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J.L. Risler Centre de Genetique Moleculaire risler at frcgm51.bitnet
