Table 3a.

Comparison of anchor residue preference identified with automatic approach with published motifs and those using positional scanning combinatorial libraries

		Pool sequencing motif					Combinatorial library motif					Automatically derived motif
System	Allele	P2	P3	P5	P6	P9	P2	P3	P5	P6	P9	P2	P3	P5	P6	P9
HLA	A*0201	LM[IVATQ]				VL[MIAT]	L[MQ]				VI[LA]	LM				VL
	A*3001	YF				L		RK			KA[LVIY]		KR			K
	A*3201	[MLITVQS]				[WIFYHT]	TMIQLVS[A]				FIYLW	MLTV				FIW
	A*6802	[LMTVATQS]				[LMTVAT]	VTS[LALMP]				VALI	TV				V
	B*0702	P				L[FWYIVMA]	P[VA]				LFAYI[M]	P				FML
	B*0801		RK	RK		LIVM			RHKF	F[RH]	LFMVIA[E]			HKR	F	FIML
	B*1501	QL				FY					FY[M]	MLQ				FY
	B*1503	QK				FY	QMK[LHASE]				F[MY]	KMQ				FY
	B*2705	R				KRLYANFMIK	R					R.	FLMWY			FIHKMLRY
	B*3501	P				YFMLI[WVA]	PA				FYM[A]	P				FMY
	B*5101	APG				VI[FWYLMA]	PA[GQVS]				I[V]	P				IV
	B*5301	P				WFL[YIVMA]	PA[IY]				FC[IW]	P				W
	B*5401	P				[FWYLIVMA]	A[P]				AV	P				A
	B*5801	AST				FW	STA[VG]				WFIY[MC]	AST				w
H-2	Db			N		LIVM			N[L]		IML[VF]			N		IML
	Dd	G	P	RK		LFI	G	P			FLI[C]	G	P			FIMLRTV
	Kd	YF				LIYM	Y				ILV[M]	Y				HIL
	Kk	E				LIVM	E[D]				IV[FL]	E				I