Bioinformatics Algorithms

CS 583 treats biological sequences (DNA, RNA, protein) as strings and asks how you design algorithms that scale when the strings are billions of characters long and the questions — "are these related?", "where does this read come from?", "what does this fold into?" — are inherently fuzzy. You'll work through the classical dynamic programming alignments (Needleman-Wunsch, Smith-Waterman) and then the indexing and k-mer machinery that makes real tools like BLAST, BWA-MEM, and minimap2 tractable, with homeworks, quizzes, and a midterm/final anchoring the load. It's a graduate algorithms course that assumes you're comfortable with complexity analysis and basic data structures; the payoff is being able to read and contribute to modern computational biology, where genome graphs and alignment-free methods are now where most of the research happens.