And now for something completely different

edwin rock epr at leland.Stanford.EDU
Tue Jun 23 16:41:32 EST 1992

	You're right, the insertion cost equation: a + bx does NOT
make much sense.  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
in an alignment of two sequences increases linearly with the PAM
distance separating them and that the following equation, where P is
the probability fo a gap of length k, fits the data accurately.

10log(P) = -36.31 + 7.44log(PAM distance) -14.93log(k).

	It's an interesting (and exciting!) paper.
	Good luck.					Edwin Rock

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