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 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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2020 |
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| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:21 |
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| Enthalten in: |
BMC bioinformatics - 21(2020), 1 vom: 24. Mai, Seite 210 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Takizawa, Hiroki [VerfasserIn] |
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| Links: |
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| Themen: |
63231-63-0 |
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| Anmerkungen: |
Date Completed 23.06.2020 Date Revised 23.06.2020 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s12859-020-3535-5 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM310303486 |
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| 100 | 1 | |a Takizawa, Hiroki |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a RintC |b fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp |
| 264 | 1 | |c 2020 | |
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| 500 | |a Date Completed 23.06.2020 | ||
| 500 | |a Date Revised 23.06.2020 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a 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 | ||
| 520 | |a 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 | ||
| 520 | |a CONCLUSION: These results demonstrate that the proposed method is applicable to long RNAs | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Accuracy-guaranteed numerical computation | |
| 650 | 4 | |a Dynamic programming | |
| 650 | 4 | |a Interval arithmetic | |
| 650 | 4 | |a RNA secondary structure | |
| 650 | 4 | |a Ribosomal RNA. | |
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| 650 | 7 | |a RNA |2 NLM | |
| 650 | 7 | |a 63231-63-0 |2 NLM | |
| 700 | 1 | |a Iwakiri, Junichi |e verfasserin |4 aut | |
| 700 | 1 | |a Asai, Kiyoshi |e verfasserin |4 aut | |
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