An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

Table 2 MSA coverage by shRNAs

^a MSA	^b NSI	^c VV	^d W	^e E	^f SV	^g ST-SV	^h PC -SV (%)	ⁱ ST-DV	^j PC-DV (%)
Pol Subtype B no Recombinants	747	35	1	1.36	11	712	95.31	588	78.71
Pol Group M plus Recombinants	1143	46	1	1.42	12	1088	95.18	913	79.88
Pol All Subtypes	1160	52	1	1.59	14	1102	95	916	78.97
Genome Subtype B no Recombinants	760	35	1	1.35	12	728	95.79	599	78.82
Genome Group M plus Recombinants	1153	46	1	1.41	12	1098	95.22	918	79.62
Genome All Subtypes	1169	52	1	1.60	13	1107	94.7	920	78.69
ZDV-3TC-EFV	1185	27	1	1.27	10	1169	98.65	1013	85.49
	1201	30	2	1.52	14	1177	98	926	77.1
	1348	53	3	1.94	13	1303	96.66	741	54.97
2299_resistant_isolates	1547	26	1	1.72	14	1552	98.84	1255	80.86
D4T-3TC-NVP	79	13	1	1.9	4	68	86.08	52	65.82
ZDV-3TC-ABC	52	10	1	1.78	3	41	78.85	33	63.46
ZDV-3TC-NVP	0	0	0	0	0	0	0	0	0

^a MSA, multiple sequence alignment
^b NSI, number of sequences included in the analysis (sequences having gaps and ambiguous codons were discarded)
^c VV, total number of viral variants (these last defined as those having nucleotide changes with respect to HXB2)
^d W, number of selected windows throughout the MSA, with a score threshold of 2 (windows satisfied specific requirements, see Methods)
^e E, entropy per window
^f SV, number of subdominant variants (are sequences that appear more than 4 times in an MSA, see Methods)
^g ST-SV, sequences targeted by the group of subdominant variants.
^h PC-SV, percentage of coverage by SV
^I ST-DV, number of sequences targeted by the dominant variant.
^j PC-DV, percentage of coverage by the dominant variant

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