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Table 2 MSA coverage by shRNAs

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

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