Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines

Table 2 Example conservancy analysis of a discontinuous sequence

	Reference sequence¹										Identity²
Source	F	X	X	X	D	F	F	X	X	V	No.	(%)
Strain 1	Y	L	P	S	D	F	F	P	S	I	3	(60)
Strain 2	F	L	P	S	D	F	F	P	S	V	5	(100)
Strain 3	R	L	P	S	K	Q	F	P	S	V	2	(40)
Strain 4	Y	E	P	T	D	F	F	P	S	V	4	(80)
Strain 5	F	L	P	T	D	F	F	P	S	V	5	(100)
Strain 6	F	L	P	T	D	F	S	F	T	V	4	(80)
Strain 7	F	L	P	S	D	F	F	P	S	V	5	(100)
Strain 8	Y	E	P	S	E	F	S	F	S	I	1	(20)
Strain 9	F	L	P	S	E	F	F	P	S	V	4	(80)
Strain 10	F	L	P	S	D	F	F	P	S	V	5	(100)
Total: conservancy at identity threshold ≥ 80%											7	(70)
Total: variability at identity threshold <80%											3	(30)

1. Residues that are not defined in the reference sequence are highlighted in italics. Residues that are different from that of the corresponding residue in the reference sequence are highlighted in bold.
2. Identity indicates the number (%) of residues in the homologous sequence that are identical to the corresponding residue in the reference sequence. Residues highlighted with gray shading are not considered in calculating the identity because they are not defined in the reference sequence.
3. Totals indicate the number (%) of strains in which the reference sequence is found with an identity above or below the indicated threshold.

ISSN: 1471-2105