Manolis Kellis
@manoliskellis1·24.9K subscribers·255 videos
MIT CompBio Lecture 17 - Comparative Genomics
Posted
November 9, 2018
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November 9, 2018
2,108
34
1.61%
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1:20:02Now PlayingMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Fall 2018
Lecture 17 - Comparative Genomics 1 - Evolutionary Signatures
1. Nucleotide conservation: evolutionary constraint
- Purifying selection, neutral branch length, discovery power
- Detect constrained elements: nucleotides, windows, HMM
- Estimate fraction constrained: signal vs. background
2. Evolutionary signatures: focus on pattern of change
- Different functions == Characteristic patterns of evolution
3. Signatures of protein-coding genes
- Reading-frame conservation, codon-substitution frequency
- Likelihood ratio framework: Estimating QCQN, scoring
- Revise genes, read-through, excess constraint regions
4. Signatures of RNAs, motifs, TFBS, microRNAs
- RNAs: Phylo-SCFGs. Motifs: MCS. TFBS: branch length
- miRNAs: Struct/evo. Comb: decision trees, random forests
- Sense/anti-sense miRNAs, mature/star arm cooperation
5. Measuring selection within the human lineage
Slides for Lecture 17 are at:
)/Lecture17_ComparativeGenomics_6up.pdf
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