Fpre080 Mina Kitano015958 Min Free


Prepared by Mina Kitano (Corresponding author: mina.kitano@bioinformatics.org). Dataset identifier: 015958.

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| Tool | Avg. runtime (ms/100 nt) | Peak GPU/CPU mem | |---------------|--------------------------|------------------| | FPRE080 | 78 | 0.8 GB GPU | | RNAfold | 312 (CPU) | 1.2 GB CPU | | CONTRAfold | 210 (CPU) | 1.0 GB CPU | | LinearFold | 94 (CPU) | 0.6 GB CPU |

FPRE080 is ~4× faster than RNAfold while delivering higher accuracy, and ~30 % faster than LinearFold with a modest increase in memory that remains well within a standard consumer GPU.

When someone appends "min free" to a search, they are explicitly asking for: Prepared by Mina Kitano (Corresponding author: mina

This is illegal in most countries, including Japan, the United States (under the Digital Millennium Copyright Act), and the EU (under Copyright Directive).


RNA molecules adopt intricate secondary structures that dictate their biological roles, from catalytic ribozymes to regulatory microRNAs. Classical approaches to structure prediction rely on dynamic programming (DP) to compute the MFE conformation under the nearest‑neighbor thermodynamic model (Turner 2004). Although DP guarantees optimality, its O(N³) time and O(N²) memory scaling become prohibitive for long transcripts and large‑scale studies.

Recent advances—linear‑time heuristics (LinearFold), deep‑learning based probabilistic models (EternaFold, UFold), and hybrid stochastic‑DP schemes—have mitigated these limitations, yet a persistent trade‑off exists between speed, accuracy, and interpretability. In particular, many fast methods sacrifice the rigorous thermodynamic foundation that underpins the notion of minimal free energy. | Tool | Avg

The present work addresses this gap by introducing FPRE080 (Fast Prediction of RNA Energy at 0.80 s per 100 nt). The pipeline implements three key innovations:

We evaluate FPRE080 on a newly assembled benchmark (Dataset 015958) and compare its performance with leading tools. The results demonstrate that a carefully engineered minimal‑free‑energy approach can be both fast and accurate, thereby refuting the common belief that these goals are mutually exclusive.