Instructor: Prof. Steven Salzberg, 3125
Biomolecular Sciences Building
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
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.
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
contact Professor Salzberg directly.
counts as a "core" course for the Computer Science Ph.D. requirement.
schedule and syllabus (updated continuously throughout the semester)
listing at U. Maryland's Testudo site (NOTE: Testudo once again has the wrong
building and room number!)
Grades will be
determined by performance on homework assignments, class
presentations, a final exam, and a small project.
Course meeting time and
location for Fall
and Thursdays, 2:00-3:15pm, Room 3118 Biomolecular Sciences Bldg.
Textbook: Computational Gene
Prediction (CGP) by William H. Majoros
Supplemental texts, free online at the NCBI
Bookshelf (click title to view):
the Cell, by Bruce
Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
and Peter Walter. Garland Publishing, 2002.
Brown, BIOS Scientific Publishers, 2002.