Table 1 SsNA secondary structure prediction tools included in the present study
From: Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools
Method | Year | Prediction approach | ssDNA parameter | Pseudoknots | Speed |
|---|---|---|---|---|---|
Mfold | 2003 | MFE-based | Yes | No | \(O(n^3)\) |
RNAfold | 2008 | MFE-based | Yes | No | \(O(n^3)\) |
CentroidFold | 2009 | MFE-based or knowledge-based with \(\gamma\)-centroid estimator | No | No | \(O(n^3)\) |
LinearFold | 2019 | MFE-based or knowledge-based with runtime linearization and heuristic beam search | No | No | O(n) |
CONTRAfold | 2006 | Machine learning | No | No | \(O(n^3)\) |
MC-fold | 2008 | Machine learning | No | Yes | \(O(n^{{}^{15}/{}_{2}})\) |
MXfold2 | 2021 | Deep learning & thermodynamic | No | No | 0.31 s (GPU)a |
UFold | 2022 | Deep learning | No | Yes | 0.16 s (GPU)a |
SPOT-RNA | 2019 | Deep learning | No | Yes | 77.80 s (GPU)a |