LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

@article{Zhang2020LinearPartitionLA,
  title={LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities},
  author={H. Zhang and L. Zhang and D. Mathews and L. Huang},
  journal={Bioinformatics},
  year={2020},
  volume={36},
  pages={i258 - i267}
}
  • H. Zhang, L. Zhang, +1 author L. Huang
  • Published 2020
  • Mathematics, Computer Science, Biology, Physics, Medicine
  • Bioinformatics
Abstract Motivation RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more… Expand
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