Faster computation of exact RNA shape probabilities
Janssen S, Giegerich R (2010)
Bioinformatics 26(5): 632-639.
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| Veröffentlicht | Englisch
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Abstract / Bemerkung
Motivation: Abstract shape analysis allows efficient computation of a representative sample of low-energy foldings of an RNA molecule. More comprehensive information is obtained by computing shape probabilities, accumulating the Boltzmann probabilities of all structures within each abstract shape. Such information is superior to free energies because it is independent of sequence length and base composition. However, up to this point, computation of shape probabilities evaluates all shapes simultaneously and comes with a computation cost which is exponential in the length of the sequence.
Results: We device an approach called RapidShapes that computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its share of Boltzmann probability. This aims at a heuristic improvement of runtime, while still computing exact probability values.
Conclusion: Evaluating this approach and several substrategies, we find that only a small proportion of shapes have to be actually computed. For an RNA sequence of length 400, this leads, depending on the threshold, to a 10-138 fold speed-up compared with the previous complete method. Thus, probabilistic shape analysis has become feasible in medium-scale applications, such as the screening of RNA transcripts in a bacterial genome.
Availability: RapidShapes is available via http://bibiserv.cebitec.uni-bielefeld.de/rnashapes
Contact: robert@techfak.uni-bielefeld.de
Erscheinungsjahr
2010
Zeitschriftentitel
Bioinformatics
Band
26
Ausgabe
5
Seite(n)
632-639
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1893946
Zitieren
Janssen S, Giegerich R. Faster computation of exact RNA shape probabilities. Bioinformatics. 2010;26(5):632-639.
Janssen, S., & Giegerich, R. (2010). Faster computation of exact RNA shape probabilities. Bioinformatics, 26(5), 632-639. https://doi.org/10.1093/bioinformatics/btq014
Janssen, Stefan, and Giegerich, Robert. 2010. “Faster computation of exact RNA shape probabilities”. Bioinformatics 26 (5): 632-639.
Janssen, S., and Giegerich, R. (2010). Faster computation of exact RNA shape probabilities. Bioinformatics 26, 632-639.
Janssen, S., & Giegerich, R., 2010. Faster computation of exact RNA shape probabilities. Bioinformatics, 26(5), p 632-639.
S. Janssen and R. Giegerich, “Faster computation of exact RNA shape probabilities”, Bioinformatics, vol. 26, 2010, pp. 632-639.
Janssen, S., Giegerich, R.: Faster computation of exact RNA shape probabilities. Bioinformatics. 26, 632-639 (2010).
Janssen, Stefan, and Giegerich, Robert. “Faster computation of exact RNA shape probabilities”. Bioinformatics 26.5 (2010): 632-639.
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2019-09-06T08:54:16Z
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