Gaps and PAMs (estimating deletion penalty parameters)

Gaston Gonnet gonnet at inf.ethz.ch
Wed Jul 1 04:23:33 EST 1992

In article <1992Jun30.024538.3684 at gpu.utcs.utoronto.ca> lamoran at gpu.utcs.utoronto.ca (L.A. Moran) writes:
>     "subjective decisions about the values of gaps is what has been 
>      done until recently. We have now given a model under which parameters
>      can be computed from the available samples. I am afraid that you
>      tend to imply that alignment is "black magic" or "art". I disagree
>      strongly with this view. We should establish models, compute the
>      parameters for these models, verify/reject the models against reality
>      and move into better models when the old ones become unsuitable to
>      describe reality. This is the way that science makes progress, not
>      with "subjective measures".  There are hundreds of examples of this
>      methodology in science."
>With all due respect, I do not consider your "model" to be entirely objective.
>I still believe that estimating the value of gaps is a difficult problem
>that ultimately boils down to a "guesstimate".
Have you read our paper on insertion/deletions?  Or is this your
"guess" on its contents?  Yes, I agree it is a difficult problem,
we have taken the first crack at it, progress is to be expected.
Would you like to have a copy?

Gaston H. Gonnet, Informatik, ETH, Zurich.

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