Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Methodology article

RNAalifold: improved consensus structure prediction for RNA alignments

Stephan H Bernhart1*, Ivo L Hofacker2, Sebastian Will3, Andreas R Gruber2 and Peter F Stadler1245

Author Affiliations

1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany

2 Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria

3 Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee, Geb. 106, D-79110 Freiburg, Germany

4 RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI) Perlickstrasse 1, D-04103 Leipzig, Germany

5 The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, New Mexico

For all author emails, please log on.

BMC Bioinformatics 2008, 9:474  doi:10.1186/1471-2105-9-474

Published: 11 November 2008

Additional files

Additional file 1:

Additional results. Results of various unsuccessful approaches to increase the accuracy of RNAalifold.

Format: PDF Size: 12KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Stochastic backtracking. Detailed description of stochastic backtracking algorithm for consensus structure prediction using RNAalifold.

Format: PDF Size: 36KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Datasets. List of the datasets used for evaluating performance.

Format: PDF Size: 28KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Alignment and structure of SNORD86. The Rfam alignment and reference structure of SNORD86 together with the energies of the structure on the single molecules.

Format: PDF Size: 14KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Enterovirus 5' cloverleaf structure. Analysis of the effects leading to better prediction of the Enterovirus 5' cloverleaf structure.

Format: PDF Size: 32KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

GcvB structure. Analysis of the effects leading to better prediction of the GcvB structure.

Format: PDF Size: 27KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Snake H/ACA snoRNA structure. Analysis of the effects leading to better prediction of the Snake H/ACA snoRNA structure.

Format: PDF Size: 77KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Hammerhead Rybozyme structure. Analysis of the effects leading to better prediction of the Hammerhead Rybozyme structure.

Format: PDF Size: 108KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

R2 RNA element structure. Analysis of the effects leading to better prediction of the R2 RNA element structure.

Format: PDF Size: 62KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10:

UnaL2 LINE 3' element structure. Analysis of the effects leading to better prediction of the UnaL2 LINE 3' element structure.

Format: PDF Size: 142KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data