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LinAliFold and CentroidLinAliFold: Fast RNA consensus secondary structure prediction for aligned sequences using beam search methods
Open accessPreprint — published as 10.1093/bioadv/vbac078 · Paper page
Abstract
RNA consensus secondary structure prediction from aligned sequences is a powerful approach for improving the secondary structure prediction accuracy. However, because the computational complexities of conventional prediction tools scale with the cube of the alignment lengths, their application to long RNA sequences, such as viral RNAs or long non-coding RNAs, requires significant computational time. In this study, we developed LinAliFold and CentroidLinAliFold, fast RNA consensus secondary structure prediction tools based on minimum free energy and maximum expected accuracy principles, respectively. We achieved software acceleration using beam search methods that were successfully used for fast secondary structure prediction from a single RNA sequence. Benchmark analyses showed that LinAliFold and CentroidLinAliFold were much faster than the existing methods while preserving the prediction accuracy. As an empirical application, we predicted the consensus secondary structure of coronaviruses with approximately 30,000 nt in 5 and 76 minutes by LinAliFold and CentroidLinAliFold, respectively. We confirmed that the predicted consensus secondary structure of coronaviruses was consistent with the experimental results. The source code is freely available at https://github.com/fukunagatsu/LinAliFold-CentroidLinAliFold .
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Metadata
- Authors
- Fukunaga, T., & Hamada, M.
- Affiliations
- Waseda University (JP)
- Corresponding author
- Fukunaga, Tsukasa
- Venue
- Bioinformatics Advances
- Publisher
- openRxiv
- Published
- 2022-06-17
- Volume
- 2
- Issue
- 1
- Pages
- vbac078-vbac078
- ISSN
- 2635-0041 (ISSN-L)
- PMC
- PMC9710674
- OpenAlex
- W4307137870
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 1
- FWCI
- 0.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Bioinformatics Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- University of Tokyo
- Japan Society for the Promotion of Science (19K20395, JP20H05582, 22H04925, JP22H04891)
- Institute of Medical Science, University of Tokyo
- Institute of Genetics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- beam search, minimum free energy, computational efficiency, long non-coding RNA, viral RNA, RNA secondary structure
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