Table 2

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

index

EMBL

RNAbor

RNAborMEA

RNAbor-Sample

RNAlocopt

RNAshapes

UNAFold


0

AL591981/205922-205823

-9.0

5.0

-9.0

-8.5

-9.0

-9.0

1

CP000764/271074-271175

-43.5

5.0

-37.5

-44.5

-23.0

-53.0

2

CP000764/308099-308200

-27.0

-18.0

-24.5

-31.5

-25.5

-22.0

3

BA000028/760473-760574

-25.5

-0.5

-36.0

-38.5

-24.5

-31.0

4

CP000557/252200-252301

-9.5

8.5

-9.5

8.5

-10.0

-12.0

5

X83878/168-267

60.0

87.5

57.0

66.0

64.0

59.0

6

BA000004/1593074-1592973

35.0

16.5

-13.5

-21.5

-19.0

-13.5

7

AAOX01000023/19446-19345

-15.0

-2.0

-13.0

-18.5

-13.5

-15.5

8

CP000416/1798040-1798138

5.5

1.5

1.5

12.0

4.5

-4.5

9

CP000721/398929-399026

26.0

24.5

16.5

-20.0

21.5

-32.0

10

BA000028/1103943-1104044

1.0

1.5

2.0

-0.5

0.5

0.5

11

ABDQ01000002/251055-251152

-16.0

-2.5

-16.5

-21.5

-17.5

-22.5

12

AAXV01000026/31334-31233

11.5

6.0

-1.5

-8.5

22.0

-3.0

13

AE016877/298774-298875

-18.5

14.0

-17.5

-34.0

-12.0

-26.5

14

BA000004/676475-676576

-28.5

-31.0

-28.0

-69.0

-21.0

-29.5

15

AE017333/692981-693082

-1.5

2.5

-11.5

-9.5

-5.5

-53.0

16

AM180355/256217-256318

-17.0

-45.0

-45.5

-49.0

-48.0

-49.0

17

AM406671/1321062-1320965

-25.5

-15.0

-22.0

-28.5

-23.5

-23.5

18

CP000612/2598111-2598012

-42.0

-39.5

-42.0

-47.5

-39.0

-38.5

19

CP000002/697032-697134

-8.0

-11.0

-10.5

-10.0

-4.5

-7.5

20

CP000002/2295936-2295837

23.5

47.0

31.5

21.0

30.0

22.5

21

AL596170/223345-223246

-0.5

7.0

0.5

-8.5

-10.0

-10.0

22

ABDQ01000005/131908-131807

-33.0

-15.5

-31.5

-31.5

-19.0

-50.0

23

AAOX01000052/9069-8968

-13.5

1.5

-14.0

-21.0

-15.5

-14.5

24

AE017333/4024324-4024425

-29.5

-26.5

-33.5

-24.0

-23.5

-36.0

25

AP006627/1554717-1554818

-31.5

-1.5

-37.0

-44.5

-28.5

-43.5

26

CP000024/1182948-1183043

-0.5

-18.5

-9.0

4.0

2.0

-19.0

27

BA000028/786767-786867

-18.0

-41.5

-48.0

-46.5

-49.0

-44.5

28

ABDP01000002/29688-29587

-34.5

-42.5

-34.5

-37.0

-35.0

-50.0

29

BA000043/272473-272574

-9.5

4.0

-9.5

-10.0

-3.0

-12.5

30

CP000724/944285-944386

-30.5

-21.5

-30.5

-28.5

-26.5

-31.5

31

CP000764/1409725-1409826

14.0

-3.0

-18.0

-24.0

-11.5

-20.0

32

AAEK01000017/86437-86538

-44.5

-44.0

-41.5

-52.0

-35.0

-49.0

33

CP000764/357645-357544

11.0

-13.5

-33.0

-26.0

-18.5

-36.0


NestedAlign similarity scores between the GENE ON 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 5, 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