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Algorithms for Structure and Motion in Biology
CS273 Serafim Batzoglou & Jean-Claude Latombe Final Presentation by Daniel Woods May 31, 2005
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Protein Structure Alpha Helices, Beta Sheets, Loops…
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RNA Structure RNA structure is very different from protein structure!
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Proteins and RNA
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“Functional” RNA Basic Examples…
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Another Example… “Group I Introns”
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RNA Secondary Structure
Region of Study
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RNA Sequence Alignment
Problem 1:
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RNA Sequence Alignment
Problem 2:
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RNA Sequence Alignment
STRUCTURE RNA Sequence Alignment ! Problem 2:
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Remember Threading? RNA RNA helices
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“Tree” Simplification
O(mn) Alignment Now Possible! (Liu, et al)
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Pseudoknots
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Secondary Structure Representation
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Secondary Structure Representation
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A New Perspective Used rna_match (Collins et al)
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Searching for Structures
Not much luck… …hey…let’s try making our own!
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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
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ComRNA Example Results
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ComRNA Example Results
Predicted Correct 52.6% Correct Overall, 27.9% of Helices Correct)
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ComRNA Example Results
Predicted Correct 51.4% Correct Overall, 22.7% of Helices Correct)
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MFOLD Example Results Predicted Correct
57.6% Correct Overall, 55.9% of Helices Correct)
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MFOLD Example Results Predicted Correct
56.2% Correct Overall, 57.3% of Helices Correct)
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MFOLD Example Results Predicted Correct
52.9% Correct Overall, 46.6% of Helices Correct)
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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
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Thank You!
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