Table 2.

Comparison of the genes annotated and those predicted by ZCURVE_CoV 1.0, for the SARS-CoV, TOR2 strain

Genes annotated					Genes predicted by ZCURVE_CoV 1.0
Start	Stop	bp	a.a.	Feature	Start	Stop	bp	a.a.	Feature
265	13,398	13,134	4377	ORF 1a	265	13,398a	13,134	4377	ORF 1a
13,398	21,485	8088	2695	ORF 1b	13,398a	21,485	8088	2695	ORF 1b
21,492	25,259	3768	1255	S protein	21,492	25,259	3768	1255	S protein
25,268	26,092	825	274	ORF 3	25,268	26,092	825	274	Sars274
25,689	26,153	465	154	ORF 4
26,117	26,347	231	76	E protein	26,117	26,347	231	76	E protein
26,398	27,063	666	221	M protein	26,398	27,063	666	221	M protein
27,074	27,265	192	63	ORF 7	27,074	27,265	192	63	Sars63
27,273	27,641	369	122	ORF 8	27,273	27,641	369	122	Sars122
27,638	27,772	135	44	ORF 9	27,638	27,772	135	44	Sars44
27,779	27,898	120	39	ORF 10	27,779	27,898	120	39	Sars39
27,864	28,118	255	84	ORF 11	27,864	28118	255	84	Sars84
28,120	29,388	1269	422	N protein	28,120	29,388	1269	422	N protein
28,130	28,426	297	98	ORF 13
28,583	28,795	213	70	ORF 14

^aThe program ZCURVE_CoV 1.0 has two options. The default option is to use the heptamer UUUAAAC as the conservative ‘slippery sequence’ to find the coronavirus −1 frameshift site [16]. Once the heptamer is found in the upstream sequence near the ending site of ORF 1a originally predicted, the ending site of ORF 1a and starting site of ORF 1b are both corrected to the frameshift site (13398 in this genome) according to this ‘slippery sequence.’ Otherwise, if this heptamer cannot be found, only the original sites predicted for ORF 1a and ORF 1b are displayed in the output file. The second option is to ignore the −1 frameshift, and the original sites predicted for ORF 1a and ORF 1b are always displayed, regardless of the existence of the heptamer UUUAAAC.