bioRxivJClub
LinearRaccess: linear-time approximation of RNA accessibility without base-pair span limits
bioRxiv · · Preprint · Open access
Otagaki, Sato
Abstract ↗AI summary
The abstract is read at the publisher; the summary is JClub's.
LinearRaccess computes RNA window accessibility deterministically in linear time without restricting base-pair span, achieving a median opening-energy error below 0.001 kcal/mol on bpRNA-1m(90).
- Why it matters: Existing RNA accessibility tools either impose base-pair span limits, rely on sampling with variance, or compute exactly at cubic time, leaving long-range interactions and long windows hard to handle.
- What they did: LinearRaccess uses beam-pruned inside-outside dynamic programming plus a difference-array aggregation step, running in O(N) time and O(Nb) memory for sequence length N and beam width b.
- The result: On bpRNA-1m(90) sequences of 100–1,000 nt (12,872 bpRNA-1m(90) sequences), it keeps median opening-energy error below 0.001 kcal/mol (0.14 kcal/mol for 700–1,000 nt) and analyzes the 29,903-nt SARS-CoV-2 genome in 419 seconds.
The findingWhy it mattersWhat they didThe result
AI summary of the abstract · may contain errors · not medical advice · read the paper.
- Open access