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Table 3 Best shRNAs targeting sequences in more than one MSA.

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

a HXB2 Coordinates

b shRNA Sequence

c Score

d Targeted MSAs

e Min_ST

f Max_ST

g Total

n2702-2725

h GCCTGAAAATCCATACAATACTCC

5

7,8,9,10

33 (7)

741 (9)

848

 

GCCTGAAAATCCATAt AATACTCC

6.5

2,9

6 (2)

223(9)

229

 

GCCTGAAAAc CCATACAATACTCC

5

2,9

4 (2)

62 (9)

66

n2333-2356

AGCAGATGATACAGTAg TAGAAGA

6

1,2,3,4,5,6

10 (1)

18 (6)

85

 

AGCAGATGATACAGTg TTAGAAGA

6

1,2,3,4,5,6

23 (1)

33 (4,6)

174

 

AGCAGATGATACAGTATTAGAg GA

3

1,2,3,4,5,6

12 (1,2)

15 (3,5)

82

 

AGCAGATGATACAGTAc TAGAAGA

6

1,2,4,5,6,10

6 (10)

17 (4,5,6)

81

 

AGCAGATGAc ACAGTATTAGAAGA

7

1,2,3,4,5,6

21 (1,2)

31 (3,4,5,6)

166

 

AGCAGATGATACAGTATTg GAAGA

6

1,2,3,4,5,6

11 (1,2)

15 (3,4,5,6)

82

 

g GCAGATGATACAGTATTAGAAGA

7

1,2,3,4,5,6

16 (1)

27 (6)

139

 

h AGCAGATGATACAGTATTAGAAGA

7

1,2,3,4,5,6,10

21 (10)

920 (6)

4854

r2556-2579

AGt CCTATTGAa ACTGTACCAGTA

2.5

9

1013 (9)

1013 (9)

1013

r2574-2597

CCAGTAAAATTAAAa CCAGGAATG

2

9, 10

60 (9)

74 (10)

208

 

h CCAGTAAAATTAAAGCCAGGAATG

3

9, 10

926 (9)

1267 (10)

3448

 

CCAGTAAAATTg AAGCCAGGAATG

2

9, 10

48 (9)

77 (10)

202

r2702-2725

GCCTGAAAATCCc TACAATACTCC

3.5

9

67

67

67

  1. a Genome position according HXB2 numbering system
  2. b In lowercase, nucleotides different from HXB2 reference genome
  3. c Score is given by the accomplishment of specific sequence features
  4. d Multiple sequence alignments numbered as follows:
  5. 1. POL_DNA_No_Recombinants
  6. 2. GENOME_DNA_No_Recombinants
  7. 3. POL_DNA_GroupM_Recombinants
  8. 4. GENOME_DNA_GroupM_Recombinants
  9. 5. POL_DNA_All_Subtypes
  10. 6. GENOME_DNA_All_Subtypes
  11. 7. ZDV-3TC-ABC
  12. 8. D4T-3TC-NVP
  13. 9. ZDV-3TC-EFV
  14. 10. 2299_Resistant_Isolates
  15. e Min_ST, Minimun number of sequences targeted in an MSA. In parenthesis, the specific number of MSA, to which targeted sequences belong.
  16. f Max_ST, Maximun number of sequences targeted in an MSA. In parenthesis, the specific number of MSA, to which targeted sequences belong.
  17. g Total number of sequences targeted in all the MSAs
  18. h shRNA sequence corresponds to HXB2 reference genome
  19. nshRNAs from these regions were found in non-resistant MSA, despite some of them might target resistant viral sequences.
  20. rshRNAs from these regions were found in resistant MSA.
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Virology Journal

ISSN: 1743-422X