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Satellite Workshop on RNA Ontology RNA 2005 Tenth Annual Meeting of the RNA Society Banff, May 23st and May 24rth.

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Presentation on theme: "Satellite Workshop on RNA Ontology RNA 2005 Tenth Annual Meeting of the RNA Society Banff, May 23st and May 24rth."— Presentation transcript:

1 Satellite Workshop on RNA Ontology RNA 2005 Tenth Annual Meeting of the RNA Society Banff, May 23st and May 24rth

2 Is there a danger, in molecular biology, that the accumulation of data will get so far ahead of its assimilation into a conceptual framework that the data will eventually prove an encumbrance ? John MADDOX, 1988.

3 All science is either physics or stamp collecting. Rutherford.

4 The bacterial ribosome : atoms (C,N, O, P) 55 proteins 3 RNA (4600 nucleotides)

5 Even with the knowledge of the quantum physics of water molecules, it would be impossible to deduce the laws of formation of waves in the sea. Ken WILSON.

6 How can we go beyond organizing data banks of Sequences,Structures,Motifs, Genomes ?

7 Are our concepts relevant ?

8 Towards a RNA ontology ?

9 Why do we bother about classification ? What are our aims ?

10 2) Extract information about 3D folding; 1) Derive accurate & meaningful alignments; 3) Derive rules for RNA evolution; 4) Search genomes for non-coding RNAs.

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12 Physical entity : base or base pair Attributes: three edges (W_C, H, S_E) Attribute: glycosidic angle (syn or anti) Non-physical entity : base pair relationship Attribute: interacting edges (ordered pair of edges) Attribute: orientations of glycosidic bonds (cis or trans)

13 Many other molecular attributes… Where to stop ?

14 Granularity within the Consortium 1.Tools for crystallographers -NDB tools -Jane Richardson (backbone) - Base pair families 2. Tools for the analysis, classification, and search of crystal structures - Backbone (Eli, Jane, …), SCOR - Annotate (Major), RNAview (NDB) - s2s (Jossinet), FR3D (Leontis)

15 Granularity within the Consortium 3.Tools for alignments -RFAM -s2s 4. Tools for 1D to 2D - Mfold, … - D. Mathews 5. Tools for 1D/2D to 3D - McSYM - Manip/Fragment

16 Comparisons of 3D structures Comparisons of sequences

17 The K-turn The C-motif

18 K-Turn

19 Sugar-edge Hoogsteen ACGU U A C G I1 I2 I1 I2 I1 I2 trans A CG U U A C G I1 (I2) I2 trans Sugar-edge I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick The K-turn motif

20 Watson-Crick I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick Cis Watson-Crick/Watson-crick G85 C97 ACGU U A C G 7 (0) trans 0 (7) (6) 801 (786) 0 (7) 0 (3) 6 (0) 11 (17) 0 (3) 3 (0)

21 Sugar-edge Hoogsteen ACGU U A C G I1 I2 I1 I2 I1 I2 trans G97 A80 ACGU U A C G 675 (673) 4 (4) 145 (145) trans (2) A98 ACGU U A C G 583 (580) 126 (125) 113 (112) trans 0 (1) - 0 (3) 1 (1) 0 (1) 1 (0) 0 (3) 0 (1) 3 (0) G79 - Trans Hoogsteen/Sugar-edge (0) 0 (2)

22 A CG U U A C G I1 (I2) I2 trans Sugar-edge A98 G81 ACGU U A C G 6 (6) trans (807) 1 (1) 1 (4) 7 (7) 0 (3) 3 (0) 640 (641) 3 (2) A80 G94 ACGU U A C G 38 (38) trans (15) 130 (130) 1 (1) Cis Sugar-edge/Sugar-edge

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24 Hoogsteen Watson-Crick ACGU U A C G I1 I4 I5 I4 I1I2 I3 trans A CG U U A C G I1 (I2) I2 trans Sugar-edge Watson-Crick I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick The C motif (I3)I3 I5 I4(I4)I4(I4) I4 I2

25 I6 A CG U U A C G i2 I3 I4 i2 I1 I5 I2 cis I3 I2 I5I6 Watson-Crick The C motif 0 (1) A CG U A C G 0 (2) 0 (16) 328 (134) 2 (0) 445 (246) 0 (182) cis 0 (12) 0 (181) 0 (1) 0 (16) U 29 (1) 0 (12) (1) G371 C390 ACG U A C G cis 0 (1) U 804 (801) (0) U375 A389 0 (1) 0 (2) 0 (2) 0 (2)

26 The C motif A CG U A C G 29 (29) 328 (327) 2 (0) cis 3 (3) 0 (1) U 444 (444) 1 (1) - - C390 A374 A CG U U A C G I1 (I2) I2 trans Sugar-edge Watson-Crick (I3)I3 I5 I4(I4)I4(I4) 0 (1) 0 (2)

27 The C motif A CG U A C G 804 (803) 1 (0) cis 0 (1) U 1 (1) - - A389 C372 0 (1) Hoogsteen Watson-Crick ACGU U A C G I1 I4 I5 I4 I1I2 I3 trans I4 I2

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