Syllabus

This course will cover fundamental algorithmic techniques in computational genomics. It is the first of a series of four courses (567, 568, 569 and 570) designed to give a comprehensive core knowledge in bioinformatics and computational biology. This course is a core requirement for BCB students. It is also meant for students in Computer Engineering and Computer Science who are interested in doing research in this area, pursue career opportunities in bioinformatics, or want to acquire some knowledge of this field.

Text

There is no prescribed text. Some supplementary material is provided as aid in studying from time to time. This may include slides and book chapters, as appropriate.

Prereqs

Computer Science 311 or equivalent. In order understand the material in this class you will need to be familiar with the basic concepts of algorithm design, including data structures, assymptotic notation, and ideas such as divide and conqure approaches to problem solving.

Topics

Introduction to Biological Sequences

Sequence Alignment

String Data Structures and Algorithms

Multiple Alignment

Database Search

Genome Assembly

Phylogenetics