Computational Biology: Sequence Alignment
Office: JEB B229
Office Hours: 8:30-10:30 MWF, 9:30-10:30 Tues, 8:30-9:30 Thurs
Textbook : Durbin, Eddy, Krogh, Mitchison, Biological Sequence Analysis, Cambridge University Press.
Design and analyze algorithms that address the computational problems posed by biological sequence data, such as DNA or protein sequences. Topics may include: comparing
sequences (from genes to genomes), database searching, multiple sequence alignment, Hidden Markov Models, phylogenetic inferencing, gene discovery and annotation,
and genome assembly.
Additional class presentation and/or paper required for graduate credit.
The emphasis in this course is on understanding the details of the algorithms, including computational complexity, time-accuracy trade-offs, and actually coding.
Projects: There will be three programming projects. Each will require a
significant, but not enormous, programming project and a 5-10 page project summary. Each
of the projects will be divided into several sub-projects to more evenly distribute the
time required. An additional paper will be required for graduate (CS515) credit.
Late Projects: Late projects will lose 10% per school/business day.
Weekends count as a single day.
Exams: There will be two midterms and a comprehensive final exam.
|3 Projects||20% each (17% each for CS515) |
|2 Midterms||10% each|