Bioinformatics Algorithms

C-113 HN, 1:10 PM - 2:25 PM
Office Hours: Mon 2:30 PM - 4:30 PM
Saad Mneimneh

Book
An Introduction to Bioinformatics Algorithms, by Jones and Pevzner

Lectures
Lecture 1: Intro to Bio and CS, DNA copying, a flavor of sequencing problems, pages 14-19, and chapter 3
Lecture 2: Algorithmic paradigms, greedy and brute force coin change, recursive Tower of Hanoi, pages 20-33
Lecture 3: Sorring, Fibonacci, Big O notation, pages 33-40
Lecture 4: Dynamic programming coin change, pages 41-50, 148-152
Lecture 5: Big-O vs small-o, dynamic programming vs divide and conquer, continue with dynamic programming, sequence alignment, pages 177-178
Lectures 6: Local alignment, overlap alignment
Lecture 7: Scoring matrices, pages 178-185, more general gap functions, see my notes here
Lecture 8: Multiple alignment, star alignment pages 186-193
Lecture 9: Space and time improvements, pages 227-240, but book has slightly different presentation than lecture, see my notes here
Lecture 10: Gene prediction, rectangle chaining, and spliced alignment, pages 200-206
Lecture 11: Genetic mapping, pages 83-96
Lecture 12: Motif Finding, pages 91-111
Lecture 13: Genome rearrangement, sorting by reversal, pages 125-135
Lecture 14: Gene sequencing, shortest superstring, Hampath and a greedy algorithm, pages 262-268
Lecture 15: Sequencing by hybridization SBH, Euler path, pages 268-274
Lecture 16: Protein sequencing, k-similarity and spectral alignment, pages 280-299
Lecture 17: Hash tables, applications to database search and repeat finding, pages 311-318
Lecture 18: Suffix trees and pattern matching, pages 320-324
Lecture 19: More applications of suffix trees, finding maximal repeats, all pair suffix-prefix problem
Lecture 20: Hidden Markov Models, Viterbi algorithm
Lecture 21: Maximum parsimony
Lecture 22: Hierarchical clustering and k-means
Lecture 23: Perfect phylogeny
Lecture 24: Distance based trees

Homework (almost biweekly)
Homework 0, summarize chapter 3 of the book, due Thu 2/2/2017
Homework 1, due Thu 2/9/2017 Solution
Homework 2, due Thu 2/23/2017 Solution
Homework 3, due Thu 3/9/2017, Solution
Homework 4, due Mon 3/3/2017, Solution
Test will be on Mon March 27 in class.
Homework 5, due Thu 4/27/2017, Solution
Homework 6, due last day of class, Solution

Grading policy
Homework 30%
Midterm 20%
Project/Report 10%
Final 40%