PPT-Lecture 10 – Models of DNA Sequence Evolution

Correct for multiple substitutions in calculating pairwise genetic distances Derive transformation probabilities for likelihoodbased methods Prob R r t p m x P mk v. Sequencing strategies. Hierarchical genome shotgun HGS – Human Genome Project. “map first, sequence second. ”. clone-by-clone … cloning is performed twice (BAC, plasmid). Sequencing strategies. Announcements. 1. st. HW posted by tonight, due next Friday at . 4pm. .. Discussion section starts next week, W 4-5, Packard 364. TA OHs start next . week (Wed 5-6pm, Fri 10-11am (Milind), Thu . 4-5pm . Hidden Markov Models for Sequence Analysis 1 . 11-15-2011. Machine . learning algorithms are a class of statistics-based algorithms that recognize patterns in data by first leaning the patterns from known examples using a . Karl Pichotta and Raymond J. Mooney. The University of Texas at Austin. ACL 2016, Berlin. 1. Event Inference: Motivation. Suppose we want to build a Question Answering system…. 2. Event Inference: Motivation. Richard Preen & Larry Bull. UWE, Bristol. Introduction. Evolutionary computing has been applied widely.. Over 70 examples of “human competitive” performance have been noted [. Koza. , 2010].. . N. umber . of differences between each pair of taxa . vs. genetic . distance between those two taxa. .. . The x-axis is a proxy for time since . divergence between . the two taxa.. . Differences . The main sequence. Evolution off the main sequence. Nucleosynthesis. PHY111. Stellar Evolution and . Nucleosynthesis. Basics. On the . Hertzsprung. -Russell Diagram. Observations. Evolution on to the Main Sequence. Stevan. J. Arnold. Oregon State University. Outline. Synthesis in evolutionary biology then and now. Simpson (1944) & the ongoing synthesis in evolutionary quantitative genetics. Two examples of the ongoing synthesis (Estes & Arnold 2007, . A talk for Hans . Zinnecker. (sort of).. Alison Sills, McMaster University. Collision Models . Sills (1997-2009), . Glebbeek. (2008-2010). head-on (S97, G08) and off-axis collisions (S01). With rotation (S05). Frank Wood fwoodstatcolumbiaeduLinear Regression Models Lecture 3 Slide 2Least Squares MaxminimizationFunction to minimize wrt Minimize this by maximizing QFind partials and set both equal to zero go 2,3,4,52,3, Pierce J. Ogden2,3,7, Patrick F. Riley George M. Church 2,3, Lucy J. Colwell 1,6 and Eric D. Kelsic2,3,4 ECHNOLOG | www.nature.com/naturebiotechnology complete (C), random (R) or additi 7. Analysing the data from the experiment. Analysing the data from the experiment. If you have organised the experimental software well, then the data will be in one or more Excel data files (or something similar).. Introduction to Biostatistics and Bioinformatics. Phylogenetics. This Lecture. Learning Objectives. Molecular . Evolution . Calculating . Distances . Clustering . Algorithms . Cladistic. . Methods . pair-wise alignment. × . multiple . sequence . alignment. Flavors of sequence alignment. global alignment . × . local alignment. global. local. align entire sequence. stretches of sequence with the highest density of matches .