Class Notes

The link to the ongoing class notes can be found here.

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Videos

If the video isn’t linked yet, check Brown Panopto or the Media Library in Canvas.

Date	Topic	Video	Extra Material
9/7/23	Welcome to CS 181!	recording	slides
9/12/23	Intro to Alignment	recording	slides
9/14/23	Global Alignment	recording	Hannah's Notes
9/19/23	Needleman-Wunsch Algorithm and BLOSUM Matrices	recording	Hannah's Notes
9/21/23	Local Alignment	recording
9/26/23	More Local Alignment + Intro to Gap Alignment	recording	Hannah's Notes
9/28/23	Affine Gap Alignment		slides
10/3/23	Sequence Alignment + Graph Theory	recording
10/5/23	Graph Algorithms	recording
10/10/23	Topological Sort	recording
10/12/23	Finishing up Alignment Applications	recording
10/17/23	Languages and DFAs	recording
10/19/23	Intro to KMP and Failure Function	recording	kmp slides failure func slids
10/24/23	More DFAs and More KMP	recording	DFA Slides NFA Slides Regex Slides
10/26/23	Failure Function and KMP DFA algorithms	recording
10/31/23	Proof of Failure Function Runtime and Intro to Suffix Trees	recording
11/2/23	Midterm <3
11/7/23	Suffix Trees and Burrows-Wheeler Transform	recording	Burrows-Wheeler Slides
11/9/23	SRC Presentation and Wrapping Up Chapter 2	recording
11/14/23	UPGMA Algorithm	recording	Phylogeny Slides
11/16/23	Neighbor-Joining Algorithm	recording	Phylogeny Slides
11/21/23	Intro to HMMs	recording
11/28/23	HMMs Continued	recording
11/30/23	Viterbi Algorithm	recording	Viterbi Slides
12/5/23	Viterbi Algorithm and Alternatives; HMMs as Generators	recording
12/7/23	Markov Chains	recording

Gear-ups

Date	Topic	Video
10/14/23	DFAs and KMP	recording