Fine-tuning structural RNA alignments in the twilight zone

Bremges A, Schirmer S, Giegerich R (2010)
BMC Bioinformatics 11(1): 222.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.
BMC Bioinformatics
Page URI


Bremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 2010;11(1): 222.
Bremges, A., Schirmer, S., & Giegerich, R. (2010). Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics, 11(1), 222.
Bremges, A., Schirmer, S., and Giegerich, R. (2010). Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics 11:222.
Bremges, A., Schirmer, S., & Giegerich, R., 2010. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics, 11(1): 222.
A. Bremges, S. Schirmer, and R. Giegerich, “Fine-tuning structural RNA alignments in the twilight zone”, BMC Bioinformatics, vol. 11, 2010, : 222.
Bremges, A., Schirmer, S., Giegerich, R.: Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 11, : 222 (2010).
Bremges, Andreas, Schirmer, Stefanie, and Giegerich, Robert. “Fine-tuning structural RNA alignments in the twilight zone”. BMC Bioinformatics 11.1 (2010): 222.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen
MD5 Prüfsumme

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

The BRaliBase dent-a tale of benchmark design and interpretation.
Löwes B, Chauve C, Ponty Y, Giegerich R., Brief Bioinform 18(2), 2017
PMID: 26984616
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.
Song Y, Hua L, Shapiro BA, Wang JT., BMC Bioinformatics 16(), 2015
PMID: 25727492
Widespread purifying selection on RNA structure in mammals.
Smith MA, Gesell T, Stadler PF, Mattick JS., Nucleic Acids Res 41(17), 2013
PMID: 23847102

33 References

Daten bereitgestellt von Europe PubMed Central.

A comprehensive comparison of comparative RNA structure prediction approaches.
Gardner PP, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15458580
Simultaneous solution of the RNA folding, alignment and protosequence problems
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Bioinformatics 21(9), 2005
PMID: 15657094
Multiple structural alignment and clustering of RNA sequences.
Torarinsson E, Havgaard JH, Gorodkin J., Bioinformatics 23(8), 2007
PMID: 17324941
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.
Harmanci AO, Sharma G, Mathews DH., BMC Bioinformatics 8(), 2007
PMID: 17445273
Alignment of RNA base pairing probability matrices.
Hofacker IL, Bernhart SH, Stadler PF., Bioinformatics 20(14), 2004
PMID: 15073017
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Local Similarity in RNA Secondary Structures
Pure multiple RNA secondary structure alignments: a progressive profile approach.
Hochsmann M, Voss B, Giegerich R., IEEE/ACM Trans Comput Biol Bioinform 1(1), 2004
PMID: 17048408
R-Coffee: a method for multiple alignment of non-coding RNA.
Wilm A, Higgins DG, Notredame C., Nucleic Acids Res. 36(9), 2008
PMID: 18420654
Multiple sequence alignment with the Clustal series of programs.
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD., Nucleic Acids Res. 31(13), 2003
PMID: 12824352
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.
Poirot O, O'Toole E, Notredame C., Nucleic Acids Res. 31(13), 2003
PMID: 12824354
Recent developments in the MAFFT multiple sequence alignment program.
Katoh K, Toh H., Brief. Bioinformatics 9(4), 2008
PMID: 18372315
Pfold: RNA secondary structure prediction using stochastic context-free grammars.
Knudsen B, Hein J., Nucleic Acids Res. 31(13), 2003
PMID: 12824339
Secondary structure prediction for aligned RNA sequences.
Hofacker IL, Fekete M, Stadler PF., J. Mol. Biol. 319(5), 2002
PMID: 12079347
RNA consensus structure prediction with RNAalifold.
Hofacker IL., Methods Mol. Biol. 395(), 2007
PMID: 17993696
ILM: a web server for predicting RNA secondary structures with pseudoknots
ConStruct: Improved construction of RNA consensus structures.
Wilm A, Linnenbrink K, Steger G., BMC Bioinformatics 9(), 2008
PMID: 18442401
Murlet: a practical multiple alignment tool for structural RNA sequences.
Kiryu H, Tabei Y, Kin T, Asai K., Bioinformatics 23(13), 2007
PMID: 17459961
A fast structural multiple alignment method for long RNA sequences.
Tabei Y, Kiryu H, Kin T, Asai K., BMC Bioinformatics 9(), 2008
PMID: 18215258
WAR: Webserver for aligning structural RNAs.
Torarinsson E, Lindgreen S., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18492721
A benchmark of multiple sequence alignment programs upon structural RNAs.
Gardner PP, Wilm A, Washietl S., Nucleic Acids Res. 33(8), 2005
PMID: 15860779
Fast and reliable prediction of noncoding RNAs.
Washietl S, Hofacker IL, Stadler PF., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15665081
Strategies for measuring evolutionary conservation of RNA secondary structures.
Gruber AR, Bernhart SH, Hofacker IL, Washietl S., BMC Bioinformatics 9(), 2008
PMID: 18302738
RNAalifold: improved consensus structure prediction for RNA alignments.
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF., BMC Bioinformatics 9(), 2008
PMID: 19014431
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J., Genome Res. 18(2), 2007
PMID: 18096747
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608160
5S Ribosomal RNA Database.
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J., Nucleic Acids Res. 30(1), 2002
PMID: 11752286


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 20433706
PubMed | Europe PMC

Suchen in

Google Scholar