CSE 584A Course Calendar, Spring 2020 (Revised)


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
Mon, Jan 13 Introduction -- Why Biosequence Analysis?
Wed, Jan 15 Introduction to Classical String Matching
Mon, Jan 20 MLK day; no class
Wed, Jan 22 Classical String Matching -- Knuth-Morris-Pratt Homework 0 (optional)
Mon, Jan 27 Classical String Matching -- Finite Automata Homework 1
Wed, Jan 29 Classical String Matching -- Aho-Corasick
Mon, Feb 3 finish up classical string matching
Wed, Feb 5 Indexing for Sublinear-Time Matching
Mon, Feb 10 Suffix Arrays in Subquadratic Time: Manber-Myers
Wed, Feb 12 Efficient Search in Suffix Arrays
Mon, Feb 17 Computing Longest Common Prefixes Homework 1 Homework 2
Wed, Feb 19 Suffix Trees and Repeat Finding
Mon, Feb 24 Finish Up Suffix Trees and Arrays
Wed, Feb 26 Pattern Matching with the Burrows-Wheeler Transform
Mon, Mar 2 Space-Efficient Indexing with the BWT
Wed, Mar 4 The Bidirectional BWT and Virtual Suffix Trees Homework 2
March 9-13 Spring break; No class
March 16-20 Coronavirus break; No class
Mon, Mar 23 The Bidirectional BWT and Virtual Suffix Trees Homework 3
Wed, Mar 25 Approximate Matching 101: the Smith-Waterman Algorithm
Mon, Mar 30 Variants of Smith-Waterman Algorithm
Wed, Apr 1 Finding Optimal Alignments in Linear Space Final Project Proposals
Mon, Apr 6 Filtering Methods for Large-Scale Approximate Matching
Wed, Apr 8 Combining Filtering with Smith-Waterman Homework 3 Homework 4
Mon, Apr 13 Approximate Matching in Indexed References: Tree Traversal
Wed, Apr 15 Speeding Up Approximate Matching in Trees
Mon, Apr 20 Bit-parallel Approximate Matching: AGREP
Wed, Apr 22 Guest lecture: Stephen Altschul Homework 4
Wed, Apr 29 Final projects due 5 PM

CSE 584A
Last update: 4/15/2020