A presentation I gave in the International Institute of Molecular and Cell Biology in Warsaw, Poland on February 10, 2010. It describes the features of the CompaRNA server (http://comparna.amu.edu.pl/).

1. bioinformatics.amu.edu.pl
CompaRNA: a server for continuous benchmarking
of automated methods for RNA structure prediction
Tomasz Puton, M.Sc.
Bioinformatics Laboratory
Institute of Molecular Biology and Biotechnology
Faculty of Biology
Adam Mickiewicz University

2. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Outline of the presentation:
1) What is CompaRNA?
2) CompaRNA features
3) Future perspectives
4) Acknowledgements

3. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Outline of the presentation:
1) What is CompaRNA?
2) CompaRNA features
3) Future perspectives
4) Acknowledgements

4. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
The CompaRNA server
A continuous benchmark of automated standalone and
web server methods for RNA secondary structure prediction.

5. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
The CompaRNA server
A continuous benchmark of automated standalone and
web server methods for RNA secondary structure prediction.
Equivalent of Livebench (http://meta.bioinfo.pl/livebench.pl)
in the field of RNA structure predition.

6. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
The CompaRNA server
A continuous benchmark of automated standalone and
web server methods for RNA secondary structure prediction.
Equivalent of Livebench (http://meta.bioinfo.pl/livebench.pl)
in the field of RNA structure predition.
The aim of CompaRNA is to assess the state of the art in the field,
provide a detailed picture of what is possible with the available tools,
where the progress is made and what major problems remain.

7. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/

8. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
Experimentally solved RNA structures

9. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures

10. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
RNA 2D METHODS

11. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
Predictions
RNA 2D METHODS

12. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
Predictions Rankings
RNA 2D METHODS

13. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
Predictions Rankings
RNA 2D METHODS
WWW

14. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
Predictions Rankings
RNA 2D METHODS
WWW

15. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
Predictions Rankings
Reference RNA secondary structures
RNA 2D METHODS
WWW

16. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
New RNAs
CompaRNA
ENGINE
RNA sequences Experimentally solved RNA structures
RNAVIEW *
Predictions Rankings
Reference RNA secondary structures
RNA 2D METHODS
WWW
* Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. (2003):
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31(13):3450-60.

17. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
CompaRNA has automatically extracted 212 RNA structures
(785 RNA chains) since February, 28 2009 from the weekly
updates of the Protein Data Bank.

18. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
CompaRNA has automatically extracted 212 RNA structures
(785 RNA chains) since February, 28 2009 from the weekly
updates of the Protein Data Bank.
357 RNA chains extracted by CompaRNA were bound to
protein chains (428 RNA chains were unbound).

19. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
14 methods predicting RNA secondary structure are tested,
including:
- Mfold
- Sfold
- Contrafold
- HotKnots, PknotsRG (can predict pseudoknots)
- McQFold

20. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
8005 secondary structure predictions have been obtained
for 785 RNA chains solved experimentally.

21. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
8005 secondary structure predictions have been obtained
for 785 RNA chains solved experimentally.
14 methods * 785 seqs of RNA chains = 10990

22. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
8005 secondary structure predictions have been obtained
for 785 RNA chains solved experimentally.
14 methods * 785 seqs of RNA chains = 10990 != 8005

23. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
8005 secondary structure predictions have been obtained
for 785 RNA chains solved experimentally.
14 methods * 785 seqs of RNA chains = 10990 != 8005
The reason for this is that various methods predicting
RNA secondary structure have different length limits of
input RNA sequences
(e.g. McQFold: 500nt, Sfold: 6000nt).

24. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
How to compare reference and predicted RNA secondary
structures in order to benchmark performance of
individual methods?

25. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
http://comparna.amu.edu.pl/
The CompaRNA server http://iimcb.genesilico.pl/comparna/
How to compare reference and predicted RNA secondary
structures in order to benchmark performance of
individual methods?
Matthews correlation coefficient

26. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Outline of the presentation:
1) What is CompaRNA?
2) CompaRNA features
3) Future perspectives
4) Acknowledgements

27. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
CompaRNA features
DEMO

28. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Outline of the presentation:
1) What is CompaRNA?
2) CompaRNA features
3) Future perspectives
4) Acknowledgements

29. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
What do I want to do next?
- test methods predicting protein-RNA interactions
- create meta-methods predicting RNA secondary
structure & protein-RNA interactions based on individual
methods
- defend my PhD thesis

30. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Outline of the presentation:
1) Introduction to the prediction of RNA structure
and protein–RNA interactions
2) The CompaRNA server – present & past
3) Future perspectives
4) Acknowledgements

31. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Acknowledgements
Janusz Kristian Łukasz
Ewa Kasia Kaja Jurek Tomek

32. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods
Thx for your attention
Questions !