Table 3

Comparison of NestedAlign similarity scores for the GENE OFF structure of the XPT guanine riboswitch

Index

EMBL

RNAbor

RNAborMEA

RNAbor-Sample

RNAlocopt

RNAshapes

UNAFold


0

AL591981/205922-205823

27.5

28.5

28.5

25.5

25.5

25.5

1

CP000764/271074-271175

13.0

12.5

11.0

6.5

12.0

5.5

2

CP000764/308099-308200

24.0

26.0

26.5

23.0

24.5

26.5

3

BA000028/760473-760574

18.5

22.0

13.0

20.5

23.5

23.0

4

CP000557/252200-252301

7.0

8.0

7.0

10.0

6.5

4.5

5

X83878/168-267

143.0

143.5

143.0

141.0

143.0

141.0

6

BA000004/1593074-1592973

41.0

39.0

41.0

36.0

38.0

41.0

7

AAOX01000023/19446-19345

47.5

45.5

46.0

42.5

34.0

43.5

8

CP000416/1798040-1798138

17.5

12.5

12.5

13.0

11.5

12.5

9

CP000721/398929-399026

36.5

20.5

23.0

-38.5

34.5

-52.5

10

BA000028/1103943-1104044

32.0

29.5

32.0

27.5

30.5

30.0

11

ABDQ01000002/251055-251152

27.0

26.0

26.5

24.0

25.5

7.5

12

AAXV01000026/31334-31233

37.5

38.5

38.0

32.5

35.0

36.0

13

AE016877/298774-298875

24.0

25.5

23.0

19.0

23.0

22.5

14

BA000004/676475-676576

9.0

4.5

6.5

-35.5

5.0

9.0

15

AE017333/692981-693082

-30.0

-9.5

-23.5

-25.5

-17.0

-70.5

16

AM180355/256217-256318

-23.5

-24.0

-25.0

-27.0

-23.5

-27.0

17

AM406671/1321062-1320965

-0.5

3.5

1.0

-10.0

1.0

0.5

18

CP000612/2598111-2598012

-12.0

-9.0

-8.0

-8.5

-9.5

-9.0

19

CP000002/697032-697134

16.5

7.0

12.0

14.0

16.5

7.5

20

CP000002/2295936-2295837

75.0

73.0

75.5

71.0

72.0

69.5

21

AL596170/223345-223246

30.5

31.5

30.5

28.5

29.5

29.5

22

ABDQ01000005/131908-131807

12.5

3.0

13.0

10.5

13.5

4.5

23

AAOX01000052/9069-8968

12.5

14.5

13.5

11.0

12.0

12.0

24

AE017333/4024324-4024425

-3.5

2.5

3.5

6.0

-2.5

-1.5

25

AP006627/1554717-1554818

22.5

18.0

22.5

14.5

25.5

12.5

26

CP000024/1182948-1183043

6.0

7.0

6.5

6.0

5.0

6.0

27

BA000028/786767-786867

-23.5

-19.5

-23.0

-24.5

-21.0

-24.0

28

ABDP01000002/29688-29587

3.0

1.0

2.5

1.0

4.5

0.5

29

BA000043/272473-272574

17.5

12.5

12.5

13.5

12.5

11.5

30

CP000724/944285-944386

10.0

11.0

10.5

7.0

12.0

9.5

31

CP000764/1409725-1409826

32.5

36.0

32.0

26.5

35.0

30.5

32

AAEK01000017/86437-86538

11.5

11.5

13.0

8.0

13.0

11.0

33

CP000764/357645-357544

23.5

22.0

24.5

24.0

22.0

22.5


NestedAlign similarity scores between the GENE OFF structure of the XPT guanine riboswitch of B. subtilis, experimentally determined using in-line probing (see [35]), and the structurally most similar secondary structure among near-optimal structures generated by each of the following six methods: RNAbor, RNAborMEA, RNAbor-Sample, RNAlocopt, RNAshapes, UNAFold. These values are plotted in Figure 6, where more details on the computational experiment are given.

Clote et al. BMC Bioinformatics 2012 13(Suppl 5):S6   doi:10.1186/1471-2105-13-S5-S6

Open Data