Skip Navigation


Bioinformatics Advance Access originally published online on July 14, 2005
Bioinformatics 2005 21(17):3516-3523; doi:10.1093/bioinformatics/bti577
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/17/3516    most recent
bti577v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (30)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Reeder, J.
Right arrow Articles by Giegerich, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Reeder, J.
Right arrow Articles by Giegerich, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

Jens Reeder and Robert Giegerich *

Faculty of Technology, Bielefeld University 33615 Bielefeld, Germany

*To whom correspondence should be addressed.

Motivation: The well-known Sankoff algorithm for simultaneous RNA sequence alignment and folding is currently considered an ideal, but computationally over-expensive method. Available tools implement this algorithm under various pragmatic restrictions. They are still expensive to use, and it is difficult to judge if the moderate quality of results is because of the underlying model or to its imperfect implementation.

Results: We propose to redefine the consensus structure prediction problem in a way that does not imply a multiple sequence alignment step. For a family of RNA sequences, our method explicitly and independently enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences. For each sequence, it delivers the thermodynamically best structure which has this common shape. Since the shape space is much smaller than the structure space, and identification of common shapes can be done in linear time (in the number of shapes considered), the method is essentially linear in the number of sequences. Our evaluation shows that the new method compares favorably with available alternatives.

Availability: The new method has been implemented in the program RNAcast and is available on the Bielefeld Bioinformatics Server.

Contact: jreeder{at}TechFak.Uni-Bielefeld.DE,robert{at}TechFak.Uni-Bielefeld.DE

Supplementary information: Available at http://bibiserv.techfak.uni-bielefeld.de/rnacast/supplementary.html

Received on May 9, 2005; revised on June 16, 2005; accepted on July 6, 2005

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief Funct Genomic ProteomicHome page
S. H. Bernhart and I. L. Hofacker
From consensus structure prediction to RNA gene finding
Briefings in Functional Genomics, November 1, 2009; 8(6): 461 - 471.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. R. Stocsits, H. Letsch, J. Hertel, B. Misof, and P. F. Stadler
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Nucleic Acids Res., October 1, 2009; 37(18): 6184 - 6193.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. O. Harmanci, G. Sharma, and D. H. Mathews
Stochastic sampling of the RNA structural alignment space
Nucleic Acids Res., July 1, 2009; 37(12): 4063 - 4075.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Smit, R. Knight, and J. Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition
Nucleic Acids Res., April 1, 2009; 37(5): 1378 - 1386.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. K. Mimouni, R. B. Lyngso, S. Griffiths-Jones, and J. Hein
An Analysis of Structural Influences on Selection in RNA Genes
Mol. Biol. Evol., January 1, 2009; 26(1): 209 - 216.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. Abraham, O. Dror, R. Nussinov, and H. J. Wolfson
Analysis and classification of RNA tertiary structures
RNA, November 1, 2008; 14(11): 2274 - 2289.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
K. Katoh and H. Toh
Recent developments in the MAFFT multiple sequence alignment program
Brief Bioinform, July 1, 2008; 9(4): 286 - 298.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Torarinsson and S. Lindgreen
WAR: Webserver for aligning structural RNAs
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W79 - W84.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Lindgreen, P. P. Gardner, and A. Krogh
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
Bioinformatics, December 15, 2007; 23(24): 3304 - 3311.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
E. S. Andersen, A. Lind-Thomsen, B. Knudsen, S. E. Kristensen, J. H. Havgaard, E. Torarinsson, N. Larsen, C. Zwieb, P. Sestoft, J. Kjems, et al.
Semiautomated improvement of RNA alignments
RNA, November 1, 2007; 13(11): 1850 - 1859.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Kiryu, Y. Tabei, T. Kin, and K. Asai
Murlet: a practical multiple alignment tool for structural RNA sequences
Bioinformatics, July 1, 2007; 23(13): 1588 - 1598.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Torarinsson, J. H. Havgaard, and J. Gorodkin
Multiple structural alignment and clustering of RNA sequences
Bioinformatics, April 15, 2007; 23(8): 926 - 932.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Voss
Structural analysis of aligned RNAs
Nucleic Acids Res., November 14, 2006; 34(19): 5471 - 5481.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Steffen, B. Voss, M. Rehmsmeier, J. Reeder, and R. Giegerich
RNAshapes: an integrated RNA analysis package based on abstract shapes
Bioinformatics, February 15, 2006; 22(4): 500 - 503.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.