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Table 2.

Comparison of Sequence Preprocessing Methods in Various Domain Groups

			Training set			Test set			Total

Group			tp		fp		fn		tn		tp		fp		fn		tn		tp		fp		fn		tn

EGF-like domain		S		281		13		10		34988		134		13		11		17488		415		22		21		52480

		R		291		5		0		329		145		4		0		136		436		7		0		467

Fibronectin III Domain		S		214		1		23		35054		100		12		13		17521		325		11		25		52577

		R		237		1		0		507		113		0		0		228		350		2		0		734

Sushi domain (SCR repeat)		S		105		0		1		35186		59		5		0		17582		165		0		0		52938

		R		106		0		0		77		59		0		0		32		165		0		0		109

ANK repeat		S		98		0		4		35190		55		52		2		17539		151		3		6		52778

		R		99		1		3		56		54		0		1		22		155		2		2		77

ABC transporters		S		530		0		0		34762		239		0		0		17407		769		0		0		52169

		R		530		3		0		90		239		2		0		43		769		1		0		137

WD repeat		S		184		3		6		35099		77		40		0		17529		261		3		6		52668

		R		186		2		4		168		76		0		1		92		262		2		5		260

[i] S = whole sequence vs. R = regions.