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Table 2 Stacking grammar specifications.

From: Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

  

Parameters

  

Grammar

NT

Total

Tied

C. elegans LSU Memory (MB)

Notes

G2

2

287(281)

283(278)

53.2

ambiguous

G7

5

341(326)

289(281)

128

min 1 nt loop; no lone pairs; no ε string

G8

4

347(334)

287(280)

103

min 1 nt loop; no lone pairs

G6S

3

282(276)

282(276)

79.4

min 2 nt loop; no ε string

  1. Stacking adds to grammars more nonterminals (NT) and total (free) parameters. This translates into increased memory requirements, as shown by the folding of C. elegans large subunit ribosomal RNA (3662 nucleotides). It also may introduce other restrictions such as not permitting lone pairs.