Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT CompBio Lecture 02 - DynamicProgramming (Part1)
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October 3, 2018
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October 3, 2018
13,128
126
11
1.04%
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40:48Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Fall 2018
Computational, Biology, Genomes, Networks, Evolution, Health, MIT, HST, Broad, CompBio
Lecture 02 - Sequence Alignment / Dynamic Programming
1. Introduction to sequence alignment
- Comparative genomics and molecular evolution
- From Bio to CS: Problem formulation
- Why it’s hard: Exponential number of alignments
2. Introduction to principles of dynamic programming
- Computing Fibonacci numbers: Top-down vs. bottom-up
- Repeated sub-problems, ordering compute, table lookup
- DP recipe: (1) Parameterization, (2) sub-problem space, (3) traversal order, (4) recursion formula, (5) trace-back
3. DP for sequence alignment
- Additive score, building up a solution from smaller parts
- Prefix matrix: finite subproblems, exponential paths
- Duality: each entryprefix alignment score; pathaligmnt
4. Advanced topics: Dynamic Programming variants
- Linear-time bounded DP(heuristic). Better than O(n2)?
- Linear-space DP: Four-Russians algorithm. Total time?
Slides for Lecture 2
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