[EMBOSS] gap penalties for water

Guy Bottu gbottu at ben.vub.ac.be
Thu Dec 4 18:58:28 UTC 2003

Well, there are two ways to compute a penalty for a gap of n positions :

<gap opening penalty> + (n - 1) * <gap extension penalty>
<gap penalty> + n * <gap length penalty>

The first way is used by EMBOSS and BLAST
The second way is used by GCG, Staden and CLUSTAL
fastA used for a long time the first way, but Prof. pearson decided 
recently to shift to the second

The two methods are basically equivalent (it depends on which values you 
choose) and you can discuss at infinitam and ad nauseam which is best.

	Guy Bottu
	Belgian EMBnet Node

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