Lectures
- Slide Deck 1 : Course introduction, policies and prospective topics & basic bio
- Slide Deck 2 : Basic bio (part 2) & computational approaches to biological problems
- Slide Deck 3 : Exact pattern matching with KMP
- Slide Deck 4 : Suffix tries and suffix trees
- Slide Deck 5 : Suffix arrays; search and construction
- Slide Deck 6 : The Burrows-Wheeler transform and the FM-index
- Slide Deck 7 : Pairwise (global) sequence alignment
- Slide Deck 8 : Pairwise (local) sequence alignment
- Slide Deck 9 : Space-efficient alignment
- Slide Deck 10 : Substitution matrices
- Slide Deck 11 : Phylogenomics
- Slide Deck 12 : Genome Assembly (part 1)
- Slide Deck 13 : Genome Assembly (part 2)
- Slide Deck 14 : Some Kmerology
- Slide Deck 15 : Using k-mers for large-scale search
- Slide Deck 16 : The colored de Bruijn Graph as a sequence search index
- Final lecture — wrap-up and review session for the final.
Other links
- Least Common Ancestor (via RMQ) in linear space and constant time
- Molecular Biology of the Cell
- Transcription
- Translation