CompaRNA

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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/).

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CompaRNA

  1. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 27. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods CompaRNA features DEMO
  28. 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. 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. 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. 31. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods Acknowledgements Janusz Kristian Łukasz Ewa Kasia Kaja Jurek Tomek
  32. 32. CompaRNA: a server for continuous benchmarking of RNA structure prediction methods Thx for your attention Questions !

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