You can download the lectures here. We will try to upload lectures prior to their corresponding classes. Introduction tl;dr: Introduction to the class and some basic bio. [slides] Computational framing of Biological Problems tl;dr: Lander Waterman & SCS as examples. [slides] Exact matching and the Z-box algorithm tl;dr: Linear time exact matching [slides] Semi-numerical string matching (Rabin-Karp) tl;dr: Treating strings as numbers & hashing [slides] Suffix Tries and Suffix Trees tl;dr: The power of indexing [slides] Suffix Arrays tl;dr: binary search FTW [slides] BWT & FM-index tl;dr: Optimal search in small space [slides] Edit distance and global alignment tl;dr: How to compare strings [slides] Semi-global alignment and gap penalties tl;dr: More dynamic programming [slides] Linear Space Alignment tl;dr: Don't keep the whole matrix [slides] Phylogenomics tl;dr: Dynamic programming on trees [slides] The de Bruijn Graph tl;dr: Thinking about k-mers [slides] Efficient representation of the de Bruijn graph tl;dr: small space dBG [slides] Gene expression estimation from RNA-seq tl;dr: How to count [slides] [supplement_slides] Wrapup tl;dr: That's all folks (well, not quite all) [slides]
