Textbook: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
Grading policy: The grade will be based on the homework (50%), a midterm (20%), and a final presentation/project (30%).
Introduction (pdf of slides) and homework 1 (due September 4th)
Homework 2 (due September 11th): 2.8,2.9 in the textbook. Draw the rooted X-forest for all the hierarchies on the set X={1,2}. How many hierarchies are there on the set X={1,2,3}?
Homework 3 (due September 18th): 2.1,2.2,2.3,2.4 in the textbook. Find the optimal alignment(s) for the pair of sequences TACGAGTACGA,ACTGACGACTGAC where the boldface characters are required to be aligned. How many distinct summaries (M,X,S) can there be for the two sequences GAGG,GAT?
Homework 4 (due September 25th): Show that the distance function introduced in class is a metric.
Homework 5 (due October 2): 3.1,3.2,3.3,3.5.
Homework 6 (due October 16): Show that for the Jukes-Cantor model the probability that a pair of characters are equal + probabilitiy that they are not equal = 1. 8.1, 8.3.
Midterm: Thursday October 16th.
Homework 7 (due October 30): Show that Z=-L-Q (where Z,L,Q are as defined in class).
Mathematical and computational biology seminar
Statistics and genomics seminar
Seminars in statistical phylogenetics
Introduction to computational biology