Computational RNA secondary structure design: empirical complexity and improved methods

BMC Bioinformatics

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.

ISSN: 1471-2105