Table 4

Structures for the study of the performance of RNA-SSD as a function of primary structure constraints.

No.

Description (source)

Size (bases)

expected run time [CPU sec]

number of multiloops

number of of stems


1

VS ribozyme from Neurospora mitochondria

167

0.64

2

11

2

Bio-150-n38

172

0.53

1

9

3

Bio-150-nl4

167

12.94

2

10

4

Group II intron ribozyme D135 from Saccharomyces cerevisiae mitochondria

584

11.54

5

32

5

Bio-200-nl9

208

7.62

3

12

6

Bio-150-nl2

150

0.16

6


Set of structures used to study the correlation between the primary structure constraints and the performance of RNA-SSD. Structures with similar characteristics (such as size, number of multiloops, etc.) appear in the same group. The structure Bio-150-nl2 was included in this set because it is relatively easy to design.

Aguirre-Hern├índez et al. BMC Bioinformatics 2007 8:34   doi:10.1186/1471-2105-8-34

Open Data