College of Chemical and Life Sciences

College of Computer, Mathematical and Physical Sciences

Institute for Advanced Computer Studies

CMSC828H: Computational Gene Finding and Genome Assembly [ Fall 2010 ]

Instructor: Prof. Steven Salzberg, 3125 Biomolecular Sciences Building

Course Description

This course will introduce students to two of the key problem areas in bioinformatics and genomics, computational gene finding and genome sequence assembly. The first half of the course will address the genome assembly problem, considering both small-scale and large-scale versions as well as recent challenges arising from the sequencing of mixed populations and from the challenges created by "next-generation" DNA sequencing machines.  The second half of the course will cover the gene finding problem in the two major classes of living organisms, prokaryotes and eukaryotes. Algorithms and strategies for finding genes in the genomes of these organisms, including both ab initio and homology-based approaches, will be discussed. The course will focus on the practical computational problems that arise in current genome sequencing and analysis projects on a wide range of species. Introductory lectures will cover the necessary background material in molecular biology and genomics.

Prerequisites: CMSC 420, CMSC 435, CMSC 451, or equivalent courses from another University, or permission of the instructor. You do not need to know any molecular biology.  If in doubt about preparation, students are encouraged to contact Professor Salzberg directly.

This counts as a "core" course for the Computer Science Ph.D. requirement.

Course schedule and syllabus (updated continuously throughout the semester)

Official course listing at U. Maryland's Testudo site (NOTE: Testudo once again has the wrong building and room number!)

Class format and grading