CSE 584A Course Calendar, Spring 2018


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 17 Introduction -- Why Biosequence Analysis?
Mon, Jan 22 Introduction to Classical String Matching
Wed, Jan 24 Classical String Matching -- Knuth-Morris-Pratt
Mon, Jan 29 Classical String Matching -- Finite Automata Homework 1
Wed, Jan 31 Classical String Matching -- Aho-Corasick
Mon, Feb 5 finish up classical string matching
Wed, Feb 7 Indexing for Sublinear-Time Matching
Mon, Feb 12 Suffix Arrays in Subquadratic Time: Manber-Myers
Wed, Feb 14 Efficient Search in Suffix Arrays
Mon, Feb 19 Computing Longest Common Prefixes Homework 1 Homework 2
Wed, Feb 21 Suffix Trees and Repeat Finding
Mon, Feb 26 Finish Up Suffix Trees and Arrays
Wed, Feb 28 Pattern Matching with the Burrows-Wheeler Transform
Mon, Mar 5 Space-Efficient Indexing with the BWT
Wed, Mar 7 The Bidirectional BWT and Virtual Suffix Trees Homework 2
March 11-17 Spring break; No class
Mon, Mar 19 Approximate Matching 101: the Smith-Waterman Algorithm Homework 3
Wed, Mar 21 Variants of Smith-Waterman Algorithm
Mon, Mar 26 Finding Optimal Alignments in Linear Space
Wed, Mar 28 Filtering Methods for Large-Scale Approximate Matching
Mon, Apr 2 Combining Filtering with Smith-Waterman Final project proposals
Wed, Apr 4 Approximate Matching in Indexed References: Tree Traversal
Mon, Apr 9 Speeding Up Approximate Matching in Trees Homework 3 Homework 4
Wed, Apr 11 finish up approximate matching in trees
Mon, Apr 16 Bit-Parallel Approximate Matching: AGREP
Wed, Apr 18 Hashing Strategies for Approximate Matching I
Mon, Apr 23 Hashing Strategies for Approximate Matching II
Wed, Apr 25 TBA 3 Homework 4
Wed, May 2 Final projects due 5 PM

CSE 584A
Last update: 1/11/2018