Visualization of RNA 2D Structures - Structure/function relationships of H/ACA motifs: Analysis & Prediction
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This document discusses various software tools for visualizing and analyzing RNA 2D structures. It describes tools that can generate 2D structure representations from experimental data, predicted structures, and 3D structural models. It also discusses annotation capabilities and tools for integrating structural, functional, phylogenetic and other information. Examples are given of specific tools like VARNA, R2R and PseudoViewer and how they can be used to visualize H/ACA guide RNAs and analyze conservation and accessibility.
Visualization of RNA 2D Structures - Structure/function relationships of H/ACA motifs: Analysis & Prediction
- 1. Visualization of RNA 2D Structures Structure-Function Relationships of H/ACA Motifs Fabrice Leclerc & Yann Ponty
- 2. 2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc) 2D representations from RNA 3D structures media to display: structural, functional, phylogenetic informations, etc RNAplot jViz.RNA
- 3. 2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc) 2D representations from RNA 3D structures media to display: structural, functional, phylogenetic informations, etc S2S/Assemble VARNA
- 4. 2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc) 2D representations from RNA 3D structures medium to display: structural, functional, phylogenetic informations, etc PseudoViewer R2R
- 6. C: Stockholm (RFAM) D: Vienna (RNAfold) E: Pseudobase A: FASTA (aligned) B: CLUSTAL F: BPSEQ G: CONNECT (CT, CT2)
- 7. conformation 1 (ON) conformation 2 (OFF) VARNA Arc RIBOSWITCH graph
- 8. mutations, chemical probing data Aalberts & Jannen, RNA, 2013 base pairing 1 RNAbows
- 10. conservation VARNA*R2R * post-processingPerreault et al., PLoS One, 2011 Leclerc, Molecules, 2010 2D representation 2D representation (3D)
- 12. 3¨ guide sequence 5¨ guide sequence Kloop ACA box functional annotation H/ACA guide RNA (Archaea) VARNA RFAM: RF00065
- 13. 3¨ guide sequence 5¨ guide sequence Kloop ACA box target sequence functional annotation H/ACA guide RNA (Archaea) VARNA RFAM: RF00065
- 14. L7Ae Nop10 Cbf5 H/ACA guide RNA (Archaea) VARNA RFAM: RF00065 functional annotation
- 20. 7 H/ACA genes 11 H/ACA motifs Muller et al., NAR, 2008 Pyrococcus & Thermococcus
- 21. Muller et al., NAR, 2008
- 22. Muller et al., NAR, 2008
- 23. R2R
- 24. + -
- 27. standard and customized representations (edition, annotation) time saving for the generation of multiple representations time saving for the update of consensus structures qualitatif (quantitatif) tools to evaluate structure-function models
- 28. RFAM (VARNA), Comparative RNA Web Site & Project (RNA2DMap, CT, BPSEQ), The RNA Mapping Database - RMDB (RDAT, RNAstructure), ... packages: Vienna Package (RNAfold, RNAalifold, etc), Boulder Alignment Editor (VARNA), SAVor (RNAfold, RNAplot), S2S/Assemble 2D & 3D, Jalview 2D & 3D (VARNA, Jmol), ... recent tools: long RNAs: RNAfdl, pairing probabilities (alternative conformations): RNAbow, RNAllViewer, ...
- 29. Institut de G└n└tique & Microbiologie, Orsay Palaiseau