String Algorithms

Catalog description

Provides an in-depth look at modern algorithms used to process string data, particularly those relevant to genomics. The course will cover the design and analysis of efficient algorithms for processing enormous amounts of collections of strings. Topics will include string search; inexact matching; string compression; string data structures such as suffix trees, suffix arrays, and searchable compressed indices; and the Borrows-Wheeler transform. Applications of these techniques in genomics will be presented, including genome assembly, transcript assembly, whole-genome alignment, gene expression quantification, read mapping, and search of large sequence databases. Prerequisites: 15-151 or 15-127 or 21-128