A “dendrogram” is a binary tree that results from merging similar items in a hierarchy. In this assignment, students build a dendrogram that represents a “phylogenetic tree” of species across the animal kingdom. Starting with raw DNA strings from mitochondrial DNA obtained from https://www.ncbi.nlm.nih.gov/nuccore/, students first compare all pairs of DNA between species using the Needleman-Wunsch algorithm, with substitution costs between amino acids specified by “BLOSUM” tables obtained at ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/blosum.tar.Z. Amazingly, simply from this information, students are then able to build up the “tree of life” using Kruskal’s algorithm by merging species in descending order of similarity according to these results from Needleman-Wunsch. Students then plot this tree to visualize the results, and they programmatically extract various clusters using recursion. Among other things, students quantitatively show that humans are in a cluster with our primeate cousins, finding the cluster: [‘Bonobo’, ‘Chimpanzee’, ‘Gorilla’, ‘Human’, ‘Neanderthal’, ‘Orangutan’].
Sat 1 MarDisplayed time zone: Eastern Time (US & Canada) change
13:45 - 15:00 | |||
13:45 12mTalk | Murder MysteryHybrid Nifty Assignments Colin Sullivan Rutgers University, Steven Chen Rutgers University, Ana Paula Centeno Rutgers University | ||
13:57 12mTalk | Augmentative and Alternative Communication Device Maps AssignmentHybrid Nifty Assignments Catherine Baker Creighton University, Yasmine Elglaly Western Washington University, Kristen Shinohara School of Information | ||
14:10 12mTalk | Nifty Assignments: Particle SystemsHybrid Nifty Assignments Keith Schwarz Stanford University | ||
14:22 12mTalk | Building The Tree of Life from ScratchHybrid Nifty Assignments Christopher Tralie Ursinus College | ||
14:35 12mTalk | Music VisualizerHybrid Nifty Assignments Kevin Wayne Princeton University | ||
14:47 12mTalk | Infinite StoryHybrid Nifty Assignments Chris Piech Stanford University, Mehran Sahami Stanford University and ACM Taskforce, Yasmine Alonso Stanford University, Katie Liu Stanford University, Javokhir Arifov Stanford University, Anjali Sreenivas Stanford University, Dan Webber Stanford University, Tina Zheng Stanford University, Ngoc Nguyen Stanford University, Iddah Mlauzi Stanford University, Juliette Woodrow Stanford University |