Lightweight comparison of RNAs based on exact sequence–structure matches

Heyne S, Will S, Beckstette M, Backofen R (2009)
Bioinformatics 25(16): 2095-2102.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Heyne, Steffen; Will, Sebastian; Beckstette, MichaelUniBi; Backofen, Rolf
Abstract / Bemerkung
Motivation: Specific functions of ribonucleic acid (RNA) molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence and structure properties. In this article, we introduce a new RNA sequence–structure comparison method which maintains exact matching substructures. Existing common substructures are treated as whole unit while variability is allowed between such structural motifs. Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method ExpaRNA (exact pattern of alignment of RNA) computes the longest collinear sequence of substructures common to two RNAs in O(H·nm) time and O(nm) space, where H ≪ n·m for real RNA structures. Applied to different RNAs, our method correctly identifies sequence–structure similarities between two RNAs. Results: We have compared ExpaRNA with two other alignment methods that work with given RNA structures, namely RNAforester and RNA_align. The results are in good agreement, but can be obtained in a fraction of running time, in particular for larger RNAs. We have also used ExpaRNA to speed up state-of-the-art Sankoff-style alignment tools like LocARNA, and observe a tradeoff between quality and speed. However, we get a speedup of 4.25 even in the highest quality setting, where the quality of the produced alignment is comparable to that of LocARNA alone.
Erscheinungsjahr
2009
Zeitschriftentitel
Bioinformatics
Band
25
Ausgabe
16
Seite(n)
2095-2102
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2953311

Zitieren

Heyne S, Will S, Beckstette M, Backofen R. Lightweight comparison of RNAs based on exact sequence–structure matches. Bioinformatics. 2009;25(16):2095-2102.
Heyne, S., Will, S., Beckstette, M., & Backofen, R. (2009). Lightweight comparison of RNAs based on exact sequence–structure matches. Bioinformatics, 25(16), 2095-2102. https://doi.org/10.1093/bioinformatics/btp065
Heyne, S., Will, S., Beckstette, M., and Backofen, R. (2009). Lightweight comparison of RNAs based on exact sequence–structure matches. Bioinformatics 25, 2095-2102.
Heyne, S., et al., 2009. Lightweight comparison of RNAs based on exact sequence–structure matches. Bioinformatics, 25(16), p 2095-2102.
S. Heyne, et al., “Lightweight comparison of RNAs based on exact sequence–structure matches”, Bioinformatics, vol. 25, 2009, pp. 2095-2102.
Heyne, S., Will, S., Beckstette, M., Backofen, R.: Lightweight comparison of RNAs based on exact sequence–structure matches. Bioinformatics. 25, 2095-2102 (2009).
Heyne, Steffen, Will, Sebastian, Beckstette, Michael, and Backofen, Rolf. “Lightweight comparison of RNAs based on exact sequence–structure matches”. Bioinformatics 25.16 (2009): 2095-2102.

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