Table 2 Table listing pseudoknot classes, corresponding treewidth and resulting complexity of the folding algorithm
From: Automated design of dynamic programming schemes for RNA folding with pseudoknots
Complexities | ||||
|---|---|---|---|---|
Type | Fatgraph | Treewidth | Full Turner | All others |
H-type | ([)] | 4 | \(O\left( n^{5}\right)\) | \(O\left( n^4\right)\)(*) |
Kissing hairpins | ([)(]) | 4 | \(O\left( n^5\right)\) | \(O\left( n^4\right)\) |
“L” [12] | ([{)]} | 5 | \(O\left( n^{6}\right)\) | \(O\left( n^6\right)\) |
“M” [12] | ([{)(]}) | 5 | \(O\left( n^{6}\right)\) | \(O\left( n^6\right)\) |
4-clique | ([{<)]}> | 5 | \(O\left( n^{6}\right)\) | \(O\left( n^6\right)\) |
5-clique | ([{<A)]}>a | 5 | \(O\left( n^6\right)\) | \(O\left( n^6\right)\) |
5-chain | ({[)(][)}] | 6 | \(O\left( n^{7}\right)\) | \(O\left( n^{7}\right)\) |