Algorithms for Structure and Motion in Biology CS

Algorithms for Structure and Motion in Biology CS 273 Serafim Batzoglou & Jean-Claude Latombe Final Presentation by Daniel Woods May 31, 2005

Protein Structure Alpha Helices, Beta Sheets, Loops…

RNA Structure RNA structure is very different from protein structure!

Proteins and RNA

“Functional” RNA Basic Examples…

Another Example… “Group I Introns”

RNA Secondary Structure Region of Study

RNA Sequence Alignment Problem 1:

RNA Sequence Alignment Problem 2:

STRUCTURE RNA Sequence Alignment ! Problem 2:

Remember Threading? RNA helices

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

Pseudoknots

Secondary Structure Representation

Secondary Structure Representation

A New Perspective Used rna_match (Collins et al)

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

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

Com. RNA Example Results

Com. RNA Example Results Predicted Correct 52. 6% Correct Overall, 27. 9% of Helices Correct)

Com. RNA Example Results Predicted Correct 51. 4% Correct Overall, 22. 7% of Helices Correct)

MFOLD Example Results Predicted Correct 57. 6% Correct Overall, 55. 9% of Helices Correct)

MFOLD Example Results Predicted Correct 56. 2% Correct Overall, 57. 3% of Helices Correct)

MFOLD Example Results Predicted Correct 52. 9% Correct Overall, 46. 6% of Helices Correct)

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

Thank You!