And now for something completely different (gap costs)

Dan Davison Davison at UH.EDU
Thu Jun 25 23:42:40 EST 1992


edwin rock said:
> 	You're right, the insertion cost equation: a + bx does NOT
> make much sense.

I beg to disagree. Try reading the literature. Fitch and Smith, PNAS,
March 1985, Optimal Sequence Alignments. 


>  Gonnet, Cohen, and Benner (1992.  Science 256:1443-1445) in their
> "Exhaustive Matching of the Entire Protein Sequence Database" have
> found that the probability of a gap occurring 
> 	It's an interesting (and exciting!) paper.

It is a piece of junk. (stronger word deleted). It contains *no*
information that allows their work to be reproduced or checked in any
way. An example of something, I'm not sure what, but it is NOT a good
paper. It may be good science but you can't tell from what they wrote.

Gonnet et al. has been discussed extensively on the info-gcg list and
the upshot is that someone who has actually tested their "PAM" matrix
(it's not; just shows that they do not understand what they are
talking about, or they redefine words to mean what they want) that the
results are, at best, no better, and often worse, than the *real* PAM
120 and PAM250 matrices.

See the info-gcg list for further information.

dan

-- 
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
myself.





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