Gap penalties, PAM matrices and so on

Dan Davison Davison at UH.EDU
Fri Jun 26 15:45:24 EST 1992

Mark Cohen said:
> A final comment specifically for Dan Davidson.

Davison ( :-))
> You made a suggestion that our gap penalty did not have a length
> term (this was on the info-gcg list which I don't have direct access
> to).  We gave 3 equations  [...] where P is the probability of a gap
> of length k  [...]

I was wrong. I was looking for something like _nk_, a la the
now-infamous w = g + nr.

> Please can you make any comments or followups here or
> bionet.general, we don't have the info-gcg list.  I suspect that
> much of the adverse comment is a result of misunderstanding.

It is clear from your posting and Dr. Gonnet's that most, if not all,
of what is going on is a misunderstanding.

The "why" is another story, but irrelevant.

Thanks for the posting.

dan davison

dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison at uh.edu/DAVISON at UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to

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