Instructor: Lynda B.M. Ellis, PhD (625-9122, lynda@tc.umn.edu)
Teaching Assistant: Flora Fan (fanx0038@umn.edu)
Room: Mayo 748
Days/Credits: T, Th 9:45-11:00am (or as arranged) / 3 credits
Lab and demonstration, F 9-11am, C381 Mayo.
Office Hours/Recitation, F 10-12.
Organizational meeting:
Tuesday September 5, 2006, 9:45am in Mayo 748.
If you would like to take this course but cannot attend the organizational meeting, please contact the instructor BEFORE the meeting, since important information is discussed in this meeting.
This course is only offered in even numbered years.
Texts (in the Coffman Union Bookstore):
(required)
- Anna Tramontano (2005) The Ten Most Wanted Solutions in Protein Bioinformatics Chapman & Hall/CRC. ISBN 1-58488-491-6
- Jerry Peek, Grace Todino-Gonguet, John Strang (2001) Learning the Unix Operating System, 5th Edition. O'Reilly Press. ISBN 0-596-00261-0
- Quick Access PERL, Research and Education Association, 2000. ISBN 0-87891-328-9
(supplemental)
- Brandon and Tooze (2000) Introduction to Protein Structure, Garland Press. ISBN 0-8153-2305-0
- Tisdall, J. (2003) Mastering PERL for Bioinformatics, O'Reilly Press. ISBN 0-596-00307-2
For Whom Intended: Graduate students in Microbiology, Immunology, and Cancer Biology; Molecular Veterinary Biosciences; Biochemistry, Molecular Biology and Biophysics;
Molecular, Cellular, Developmental Biology & Genetics;
Health Informatics; Scientific Computation;Computer Science and related
fields with interest in computational methods in molecular biology. One course
in biochemistry and knowledge of the UNIX operating system are recommended.
Objectives: At the end of this course, students will have been
introduced to:
- DNA and protein sequence and protein structure databases;
- Protein sequence analysis;
- Methods for the display of sequence comparison and prediction results;
- UNIX and the Perl computer language;
- The Genetics Computer Group (GCG), EMBOSS, BioPerl and other sequence analysis programs; and
- Current literature and research problems in this area.
Course Format and Grading: There will be two 75 minute lecture sessions
each week, and one weekly laboratory/demonstration. Homework will involve computer programming and computer-based analysis of protein sequences. Each student
will write a literature review on a current technique or research problem and present this review orally, and will complete a term project involving analysis of one or more protein sequences.
Grades will be determined by mid-term examination (20%), literature review (20%), homework (20%), and term project (40%).
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