Course Syllabus
Bioinformatics Applications
The applications and concepts of computational technologies for solving problems in molecular genetics. Current programs and the principles that underlie them will be discussed. Topics include: sequence and structure databases; sequencing; mapping; sequence alignments (dynamic programming); motifs and profiles; phylogeny reconstruction; probabilistic approaches (Markov models).
PBIO 4550
Russell Malmberg
Spring 2006
Principal Course Assignments:
Readings in the textbook, and supplemental papers, will be assigned to accompany each lecture. Homework assignments will be given approximately once a week. One take home problem set will be due near the end of the first half of the semester; a second take home problem set will be due near the end of the semester. About 2/3 of the way through the semester, Graduate students will be required to turn in a report in the form of a web page, which will subsequently be demonstrated in class.
Lecture Topics: Overview; Unix, Linux, Command-Line; Local UGA Resources; NCBI, Blast, & Other Databases; File Formats, HTML; XML, Ontologies, Databases; Sequence Alignments; Probabilities, Entropy; Motifs & Profiles; Sequence Assembly; Gene Prediction; Phylogenetic Trees; Scripting; RNA and Protein Structure Prediction; Microarrays; Systems Biology.
Specific Course Requirements for Grading:
Student grades will be based on homework assignments and take home problem sets. Additionally, graduate students will be required to write a report in the form of a web page that will be demonstrated in class.
Grading Policy:
Student grades will be based on homework assignments and take home problem sets. Additionally, graduate students will be required to write a report in the form of a web page that will be demonstrated in class. The two take home problem sets will be worth 100 points each. The weekly homework assignments are worth 2 points each. The graduate student database report is worth 25 points. The final letter grade will be determined from the sum of these.
All academic work must meet the standards contained in "A Culture of Honesty". All students are responsible to inform themselves about those standards before performing any academic work.
Attendance Policy:
Students are expected to attend lectures and labs.
Required Course Material Including Texts:
The required materials include the textbook, and materials distributed through the course web site or in class. This year's textbook is Bioinformatics, Sequence and Genome Analysis, Second Edition
Makeup Exam Policy:
Since all graded materials are take-home assignments, there will be no makeup exams.