RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp

Background Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary structures. Existing methods, however, are not applicable to long RNAs owing to the...

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Vydáno v:BMC bioinformatics Ročník 21; číslo 1; s. 210 - 19
Hlavní autoři: Takizawa, Hiroki, Iwakiri, Junichi, Asai, Kiyoshi
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 24.05.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Accuracy
Accuracy-guaranteed numerical computation
Algorithms
Analysis
Bacteria
Bioinformatics
Biomedical and Life Sciences
Complexity
Computation
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Credibility
Datasets
Dynamic programming
E coli
Fourier transforms
Interval arithmetic
Life Sciences
Methodology
Methodology Article
Microarrays
Numerical analysis
Numerical stability
Overflow
Probability
Probability distribution
Probability distributions
Ribonucleic acid
Ribosomal RNA
RNA
RNA secondary structure
Stability analysis
Structural analysis
Thermal stability
Thermophilic bacteria
Dynamic programming
Ribosomal RNA
RNA secondary structure
Interval arithmetic
Accuracy-guaranteed numerical computation
ISSN:1471-2105, 1471-2105
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Shrnutí:Background Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary structures. Existing methods, however, are not applicable to long RNAs owing to their high computational complexity. Additionally, previous research has suffered from two numerical difficulties: overflow and significant numerical errors. Result In this research, we reduced the computational complexity of calculating the landscape of the probability distribution of secondary structures by introducing a maximum-span constraint. In addition, we resolved numerical computation problems through two techniques: extended logsumexp and accuracy-guaranteed numerical computation. We analyzed the stability of the secondary structures of 16S ribosomal RNAs at various temperatures without overflow. The results obtained are consistent with previous research on thermophilic bacteria, suggesting that our method is applicable in thermal stability analysis. Furthermore, we quantitatively assessed numerical stability using our method.. Conclusion These results demonstrate that the proposed method is applicable to long RNAs..
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-020-3535-5