Gap penalties, PAM matrices and so on

Fri Jun 26 07:08:00 EST 1992

        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".
J.L. Risler    Centre de Genetique Moleculaire   risler at frcgm51.bitnet

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