An Efficient Algorithm for Exploring RNA Branching Conformations under the Nearest-Neighbor Thermodynamic Model
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arXiv
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| Main Authors: | Poznanović, Svetlana, Cardwell, Owen, Heitsch, Christine |
|---|---|
| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | |
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