Scribe: D. Slotta

Today's Handouts and Announcements

• Computational Methods in Molecular Biology, pg. 340, 345-347

Today's Topics

• Morgan Gene finding system (con't)
• Sequence Types
1. Initial noncoding region
2. Initial exon
3. Internal exon
4. Intron
5. Final Exon
6. Final noncoding region
• Methods
• Decision trees
• Markov chains
• Dynamic programming
• Protein Prediction
• Markov chain / HMM
• Learning by example
• Generative: give new sequence that scores well
• Scoring: Highest score for a new sequence
• Bayesian Networks
• Nodes for random variables
• Arrows for dependencies
• Conditional probabilities for each R.V.
• Method
• Posit a structure for a model
• Fit data to structure
• Figuring out optimal structure is NP-hard.

Today's Sources

• Salzberg, Searls, and Kasif: Chapters 10 & 11