Gap penalties, PAM matrices and so on

Gaston Gonnet gonnet at inf.ethz.ch
Sun Jun 28 02:33:46 EST 1992

In article <199206262113.AA18266 at Menudo.UH.EDU> Davison at UH.EDU (Dan Davison) writes:
>So, then, "distant" means "significant"?
"significant" is related to the probability of an alignment
being derived from homology as opposed to being random.  This
is measured directly by the score of the alignment when you
use Dayhoff matrices.  So the highest the score the highest
the significance.

"distant" is related to how long ago or recently the two
sequences diverged.  This is measured in PAM units as I
explained in a recent posting.

So the two concepts are not the same.  There is some correlation,
as every time that you have a short distance then the similarity
(confidence in the homology) is very high.  Similary, for very
remote ancestry, the confidence is lower.  But in principle the
concepts are orthogonal.

Gaston H. Gonnet.  Informatik, ETH, Zurich

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