Abstract shapes of RNA

Giegerich R, Voss B, Rehmsmeier M (2004)
Nucleic Acids Research 32(16): 4843-4851.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.
Erscheinungsjahr
Zeitschriftentitel
Nucleic Acids Research
Band
32
Zeitschriftennummer
16
Seite
4843-4851
ISSN
eISSN
PUB-ID

Zitieren

Giegerich R, Voss B, Rehmsmeier M. Abstract shapes of RNA. Nucleic Acids Research. 2004;32(16):4843-4851.
Giegerich, R., Voss, B., & Rehmsmeier, M. (2004). Abstract shapes of RNA. Nucleic Acids Research, 32(16), 4843-4851. doi:10.1093/nar/gkh779
Giegerich, R., Voss, B., and Rehmsmeier, M. (2004). Abstract shapes of RNA. Nucleic Acids Research 32, 4843-4851.
Giegerich, R., Voss, B., & Rehmsmeier, M., 2004. Abstract shapes of RNA. Nucleic Acids Research, 32(16), p 4843-4851.
R. Giegerich, B. Voss, and M. Rehmsmeier, “Abstract shapes of RNA”, Nucleic Acids Research, vol. 32, 2004, pp. 4843-4851.
Giegerich, R., Voss, B., Rehmsmeier, M.: Abstract shapes of RNA. Nucleic Acids Research. 32, 4843-4851 (2004).
Giegerich, Robert, Voss, Björn, and Rehmsmeier, Marc. “Abstract shapes of RNA”. Nucleic Acids Research 32.16 (2004): 4843-4851.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
1970-01-01T00:00:00Z

83 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

RNAshapes: an integrated RNA analysis package based on abstract shapes.
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R., Bioinformatics 22(4), 2006
PMID: 16357029
Thermodynamics of RNA-RNA binding.
Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL., Bioinformatics 22(10), 2006
PMID: 16446276
Versatile and declarative dynamic programming using pair algebras.
Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 16156887
A comprehensive comparison of comparative RNA structure prediction approaches.
Gardner PP, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15458580

24 References

Daten bereitgestellt von Europe PubMed Central.

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
On finding all suboptimal foldings of an RNA molecule.
Zuker M., Science 244(4900), 1989
PMID: 2468181
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
POEMS: program for outliers elimination in multidimensional space.
Orozco M, Luque FJ., Comput. Appl. Biosci. 4(3), 1988
PMID: 3416200
Rfam: an RNA family database.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR., Nucleic Acids Res. 31(1), 2003
PMID: 12520045

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Two alternating structures of the HIV-1 leader RNA.
Huthoff H, Berkhout B., RNA 7(1), 2001
PMID: 11214176
Evaluating the predictability of conformational switching in RNA.
Voss B, Meyer C, Giegerich R., Bioinformatics 20(10), 2004
PMID: 14962925

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
SCOR: a Structural Classification of RNA database.
Klosterman PS, Tamura M, Holbrook SR, Brenner SE., Nucleic Acids Res. 30(1), 2002
PMID: 11752346

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 15371549
PubMed | Europe PMC

Suchen in

Google Scholar