1. Algorithms for Structure and Motion in Biology
CS273
Serafim Batzoglou & Jean-Claude Latombe
Final Presentation by Daniel Woods
May 31, 2005

2. Protein Structure
Alpha Helices, Beta Sheets, Loops…

3. RNA Structure
RNA structure is very different from protein structure!

4. Proteins and RNA

5. “Functional” RNA
Basic Examples…

6. Another Example…
“Group I Introns”

7. RNA Secondary Structure
Region of Study

8. RNA Sequence Alignment
Problem 1:

9. RNA Sequence Alignment
Problem 2:

10. RNA Sequence Alignment
STRUCTURE
RNA Sequence Alignment !
Problem 2:

11. Remember Threading?
RNA
RNA
helices

12. “Tree” Simplification
O(mn) Alignment
Now Possible!
(Liu, et al)

13. Pseudoknots

14. Secondary Structure Representation

15. Secondary Structure Representation

16. A New Perspective
Used rna_match
(Collins et al)

17. Searching for Structures
Not much luck…
…hey…let’s try making our own!

18. Two Very Different Candidates
MFOLD (M. Zuker)
Fast
Dynamic Programming
Does not Predict Pseudoknots
ComRNA (Y. Ji, et al)
Pair-wise (Fold and Align)
Graph-Theoretic Approach
Can Predict Any Shape

19. ComRNA Example Results

20. ComRNA Example Results
Predicted Correct
52.6% Correct Overall, 27.9% of Helices Correct)

21. ComRNA Example Results
Predicted Correct
51.4% Correct Overall, 22.7% of Helices Correct)

22. MFOLD Example Results Predicted Correct
57.6% Correct Overall, 55.9% of Helices Correct)

23. MFOLD Example Results Predicted Correct
56.2% Correct Overall, 57.3% of Helices Correct)

24. MFOLD Example Results Predicted Correct
52.9% Correct Overall, 46.6% of Helices Correct)

25. Issues Encountered Lack of Secondary Structures in Usable Formats
Manual Searching Required for Sequences
Stuff not Compiling, or Segfaulting When it Does Compile
Too Many File Formats for the Same Data

26. Thank You!