Gonnet et al., Science, gap costs

Gaston Gonnet gonnet at inf.ethz.ch
Sun Jun 28 02:47:43 EST 1992


In article <199206262017.AA08553 at Menudo.UH.EDU> Davison at UH.EDU (Dan Davison) writes:
>
>Yup. Are you sure you know how your work will be interpreted? If not,
>perhaps a posting here explaining why (or why not) your mutation
>matrix (Fig. 2, pg. 1444) should not be used in place of the PAM 250
>would be appropriate.  A lot of people are *assuming* that is what you
>meant and *are* using it that way.
===================================================
I should note that I received a copy of the article, as it appeared,
only 3 days ago.  Checking the above remark, I contemplated with
horror that Fig 2 has been mislabelled in the following way:  What
is presented in Fig 2 is a Dayhoff matrix for PAM 250, it is the
best approximation that we could compute at this time.  It says
however, "The recommended mutation matrix.." It should say "The
recommended Dayhoff matrix...".

Now, some people have immediately recognized this as a Dayhoff matrix,
which is good.  A mutation matrix has all positive entries, is diagonally
dominant and has no entry greater than 1.  So Fig 2 is not a mutation
matrix but a Dayhoff matrix.  This matrix is the one we recommend to
be used, together with our new deletion-penalty formula, for the N&W
algorithm.

Gaston H. Gonnet. Informatik, ETH. Zurich.




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