CS414/515 Computational Biology: Sequence Alignment

General Information
Spring 2017

Terence Soule
Office: JEB B229
Email: tsoule@cs.uidaho.edu
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.

Content: 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 Projects20% each (17% each for CS515)
2 Midterms10% each
Graduate Project9%