Skip Navigation



Bioinformatics Advance Access published online on November 15, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm525
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/24/3304    most recent
btm525v1
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Lindgreen, S.
Right arrow Articles by Krogh, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lindgreen, S.
Right arrow Articles by Krogh, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing

Stinus Lindgreen a,*, Paul P. Gardner a,b,{dagger} and Anders Krogh a

aBioinformatics Centre, Department of Molecular Biology, University of Copenhagen, Denmark
bMolecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Denmark

*To whom correspondence should be addressed. Mr. Stinus Lindgreen, E-mail: stinus{at}binf.ku.dk


  Abstract

Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction.

Results: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency.

Availability: Source code available from http://mastr.binf.ku.dk/

Contact: stinus{at}binf.ku.dk

Associate Editor: Prof. Dmitrij Frishman

{dagger}present address: Wellcome Trust Sanger Institute, Cambridge, UK

Received on August 20, 2007; revised on October 11, 2007; accepted on October 13, 2007

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
Brief Funct Genomic Proteomic, 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
 RNAHome page
D. Fan, P. B. Bitterman, and O. Larsson
Regulatory element identification in subsets of transcripts: Comparison and integration of current computational methods
RNA, August 1, 2009; 15(8): 1469 - 1482.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. K. Bradley, L. Pachter, and I. Holmes
Specific alignment of structured RNA: stochastic grammars and sequence annealing
Bioinformatics, December 1, 2008; 24(23): 2677 - 2683.
[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
 BioinformaticsHome page
C. B. Do, C.-S. Foo, and S. Batzoglou
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
Bioinformatics, July 1, 2008; 24(13): i68 - i76.
[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]


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.