From Visualization to Manipulation of Secondary and Tertiary RNA Structures

1
From Visualization to Manipulation of Secondary
and Tertiary RNA Structures

• Gilles Bailly University of Grenoble
• David Auber University of Bordeaux
• Laurence Nigay University of Grenoble
• France

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Introduction

• RNA (Ribonucleic Acid) a vital molecule in
  biological systems
• is made of four bases A, C, G, U
• performs a wide range of functions in biological
  systems
• contains genetic information of viruses (HIV)
• Three levels of representation
• Primary
• Secondary
• Tertiary

structure
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Introduction

• RNAthree graphical representations
• Tertiary structure
• Secondary structure
• Primary structure

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Process
Manual secondary structure of RNA
PDB files
? Automatic secondary structure of RNA
Tertiary structure of RNA
Experiment RNA extraction
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Problems

• RNA representations
• Automatic drawing of the secondary structure of
  RNA
• Interactive visualization

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Outline

• Introduction
• Visual mapping
• Automatic drawing of the secondary structure
• NAVRNA
• A system to visualize, explore and edit RNA
• Conclusion

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Visual mapping
Aesthetic criteria used by biologists

• Loops drawn as circles

• Stems drawn as straight lines

• Edge length constant

• No edge crossing

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Visual mapping
?
An RNA graph has the property to be a Sub-cubic
outer-planar bi-connected graph. It is therefore
possible to extract a tree of this structure.
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Visual mapping
?
Step 1 Build the tree
Step 3 Compute the final layout
Step 2 Draw the tree
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Automatic drawing of the secondary structure
Manual drawing
Automatic drawing Auber 06
Vienna
http//www.tbi.univie.ac.at/ivo/RNA/
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Automatic drawing
Automatic drawing Auber 06
Automatic drawing (RNAmlView) Yang 03 Flip,
rotation, translation are necessary
Yang H., Jossinet, F., Leontis, N., Chen, L.,
Westbrook, j., Berman, H. and Westhof, E.. Tools
for the automatic identification and
classification of RNA base pairs. Nucleic aids
Res., 31, pp. 3450-60, 2003.
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Outline

• Introduction
• Visual mapping
• Automatic drawing of the secondary structure
• NAVRNA
• A system to visualize, explore and edit RNA
• Conclusion

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NAVRNA
Video-projector
Camera

• Multi-display envt
• Collaboration
• Two-handed interaction

Tokens
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NAVRNA - Visualization
Tertiary structure
Secondary structure
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NAVRNA - Collaboration
Interaction is based on the  magic
table . The position of tokens are tracked by a
vision based mechanism. A tracking video camera
is fixed on the top of the table.
Tokens
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NAVRNA Two-handed interaction

• One token panning action
• Two tokens zoom rotate
• compound panning action

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NAVRNA Exploring the tertiary structure of RNA
table
wall
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NAVRNA Editing the secondary structure of RNA

• Automatic representation of the secondary
  structure of RNA
• but
• even if the drawing is close to the one expected
  by the biologists, editing could be necessary to
  obtain a perfect layout

Bending RNA branches
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NAVRNA Bending RNA branches
Step 1 Build the tree
Step 3 Compute the final layout
Step 2 Draw the tree
Step 3
Deformation of the tree
Edges size constant
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NAVRNA Bending RNA branches
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NAVRNA Collaborative deformation of a tree
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Deformation Algorithm
Propagation of the deformation
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Deformation Algorithm

• Several branches
• Collisions
• Muliples points of controls

static point
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Complexity
O(V²) - V the number of nodes
Fruchterman variation Fruchterman 91 based on a
grid of squares
O(V)
Fruchterman, T. M., J., Reingold E. M., Graph
drawing by force directed placement. Software
Practice and Experience, 21(11), pp. 1129-64,91
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Outline

• Introduction
• Visual mapping
• Automatic drawing of the secondary structure
• NAVRNA
• A system to visualize, explore and edit RNA
• Conclusion

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Conclusion

• NAVRNA
• Multi-display envt - Large visualization surfaces
• Automatic drawing of the secondary structure
  similar to the usual manual drawing by the
  biologists
• Collaborative manipulation of RNA
• Two-handed interaction
• Algorithm for deforming RNA graphs and any
  sub-cubic outer-planar bi-connected graphs

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Future work

• Perform experimental evaluation of NAVRNA with
  biologists
• Collaboration around the table
• Enrich NAVRNA
• with new two-handed interaction techniques
• with new functions
• RNA comparison
• RNA structure prediction

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• Thank you

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PDB File
Atom name
Base name (Cytosine)
Space coordinates