Evaluating the predictability of conformational switching in RNA

Voss B, Meyer C, Giegerich R (2004)
Bioinformatics 20(10): 1573-1582.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
; ;
Abstract
Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule that can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structural switching must be verified experimentally. Results: After reviewing the strategy used in paRNAss, we present recent improvements on the algorithmic level of the approach, and the results of an evaluation procedure, comprising 1500 RNA sequences. It could be shown that the paRNAss approach performs well on known examples for conformational switching in RNA. The overall number of positive predictions was small, whereas for human 3' UTRs, representing regulatory important regions, it was substantially higher than for arbitrary natural and random sequences.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Voss B, Meyer C, Giegerich R. Evaluating the predictability of conformational switching in RNA. Bioinformatics. 2004;20(10):1573-1582.
Voss, B., Meyer, C., & Giegerich, R. (2004). Evaluating the predictability of conformational switching in RNA. Bioinformatics, 20(10), 1573-1582. doi:10.1093/bioinformatics/bth129
Voss, B., Meyer, C., and Giegerich, R. (2004). Evaluating the predictability of conformational switching in RNA. Bioinformatics 20, 1573-1582.
Voss, B., Meyer, C., & Giegerich, R., 2004. Evaluating the predictability of conformational switching in RNA. Bioinformatics, 20(10), p 1573-1582.
B. Voss, C. Meyer, and R. Giegerich, “Evaluating the predictability of conformational switching in RNA”, Bioinformatics, vol. 20, 2004, pp. 1573-1582.
Voss, B., Meyer, C., Giegerich, R.: Evaluating the predictability of conformational switching in RNA. Bioinformatics. 20, 1573-1582 (2004).
Voss, Björn, Meyer, Carsten, and Giegerich, Robert. “Evaluating the predictability of conformational switching in RNA”. Bioinformatics 20.10 (2004): 1573-1582.
This data publication is cited in the following publications:
This publication cites the following data publications:

30 Citations in Europe PMC

Data provided by Europe PubMed Central.

RNA thermometers.
Narberhaus F, Waldminghaus T, Chowdhury S., FEMS Microbiol Rev 30(1), 2006
PMID: 16438677
On realizing shapes in the theory of RNA neutral networks.
Clote P, Gasieniec L, Kolpakov R, Kranakis E, Krizanc D., J Theor Biol 236(2), 2005
PMID: 15878180
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res 32(16), 2004
PMID: 15371549
A comprehensive comparison of comparative RNA structure prediction approaches.
Gardner PP, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15458580

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 14962925
PubMed | Europe PMC

Search this title in

Google Scholar