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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 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 described and discussed. The
second 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 highly polymorphic organisms. 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 permission of the instructor. CMSC
858E Algorithms for Biosequence Analysis is recommended but not
required. If in doubt about preparation, students are encouraged to
contact the instructor directly prior to the beginning of the
semester.
Course
schedule and syllabus (NOTE: this link is currently for the Spring
2006 course)
Class format
and grading
Grades will be
determined by performance on homework assignments, class
presentations, a final exam, and a course project. Projects will
involve implementation of one of the algorithms covered during the
course or a new algorithm of the student’s own design and
application of that algorithm to publicly available genome data.
Textbook: Computational Gene
Prediction (CGP) by William H. Majoros (draft textbook,
available in class)
Supplemental texts, free online at the NCBI
Bookshelf (click title to view):
Molecular
Biology of the Cell, by Bruce
Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
and Peter Walter. Garland Publishing, 2002.
Genomes,
by T.A. Brown, BIOS Scientific Publishers, 2002.
Course meeting times: Tuesdays and Thursdays,
2:00-3:15, Room 3118 Biomolecular Sciences Bldg 296. See this
link for the official schedule.
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