CSE 584A Course Calendar, Spring 2016

This is a tentative outline of lecture topics and assignment dates for the semester. Although I have tried to predict our schedule accurately, the dates on this syllabus are subject to change, depending on how quickly we cover the material.

Date Class Topic Homework Due Homework Assigned
Wed, Jan 20 Introduction -- Why Biosequence Analysis?
Mon, Jan 25 Introduction to Classical String Matching
Wed, Jan 27 Classical String Matching -- Knuth-Morris-Pratt
Mon, Feb 1 Classical String Matching -- Finite Automata Homework 1
Wed, Feb 3 Classical String Matching -- Aho-Corasick
Mon, Feb 8 finish up classical string matching
Wed, Feb 10 Indexing for Sublinear-Time Matching
Mon, Feb 15 Suffix Arrays in Subquadratic Time: Manber-Myers
Wed, Feb 17 Efficient Search in Suffix Arrays
Mon, Feb 22 Computing Longest Common Prefixes Homework 1 Homework 2
Wed, Feb 24 Suffix Trees and Repeat Finding
Mon, Feb 29 Finish Up Suffix Trees and Arrays
Wed, Mar 2 Pattern Matching with the Burrows-Wheeler Transform
Mon, Mar 7 Space-Efficient Indexing with the BWT
Wed, Mar 9 The Bidirectional BWT and Virtual Suffix Trees
March 13-19 Spring break; No class
Mon, Mar 21 Approximate Matching 101: the Smith-Waterman Algorithm Homework 2 Homework 3
Wed, Mar 23 Variants of Smith-Waterman Algort
Mon, Mar 28 Finding Optimal Alignments in Linear Space
Wed, Mar 30 Filtering Methods for Large-Scale Approximate Matching
Mon, Apr 4 Combining Filtering with Smith-Waterman Homework 3, Final project proposals Homework 4
Wed, Apr 6 Approximate Matching in Indexed References: Tree Traversal
Mon, Apr 11 Speeding Up Approximate Matching in Trees
Wed, Apr 13 finish up approximate matching in trees
Mon, Apr 18 Bit-Parallel Approximate Matching: AGREP
Wed, Apr 20 TBA 1
Mon, Apr 25 TBA 2 Homework 4
Wed, Apr 27 TBA 3
Wed, May 4 Final projects due 5 PM

CSE 584A
Last update: 1/19/2016