DM813: Algorithms for Biological Sequence Analysis (5 ECTS)

STADS: 15005201

Level
Master's level course

Teaching period

Offered according to needs.

Teacher responsible
Email: lenem@imada.sdu.dk

Timetable
There is no timetable available for the chosen semester.

Comment:
Ubegrænset deltagerantal. 2. kvartal.

Prerequisites:
None

Academic preconditions:
The contents of DM507 Algorithms and Datastructures and ST501 Science Statistics must be known.

Course introduction
To give a thorough understanding of the theory and computational techniques behind the most important algorithms in bioinformatics

Expected learning outcome
At the end of the course the student will be able to:
- use dynamic programming for pairwise alignment of DNA and protein sequences
- describe the BLAST and FASTA algorithms in short
- explain in short how the BLOSUM and PAM matrices are constructed
- construct and use simple HMMs for multiple alignment of DNA and protein sequences
- implement other simple algorithms for multiple alignment, e.g., using a guide tree
- describe strengths and weaknesses of the different kinds of alignment methods
- implement simple algorithms for constructing evolutionary trees, e.g., neighbor joining, UPGMA, and parsimony, and describe their strengths and weaknesses
- implement a suffix tree and describe some of its applications
- compute the probability of a given evolutionary tree, based on simple probabilistic models of evolution.
- implement a Metropolis algorithm for evolutionary trees - implement Gibbs sampling
- describe the basic principles of the most common methods for protein structure prediction
- implement a simple algorithm for RNA structure prediction

Subject overview
- A short introduction to the relevant parts of biology
- Sequence alignment
- Evolutionary trees
- Protein structure
- Hidden Markov Models

Literature

Meddeles ved kursets start.

Syllabus
See syllabus.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
None

Assessment and marking:
(a) Project assignment, which has to be defended at an oral examination.
(b) Oral examination, pass/fail and internal censorship by teacher.

Expected working hours
The teaching method is based on three phase model.

Forelæsninger: 25 timer
Eksaminatorietimer/opgaveregning: 10 timer
Educational activities

Language
This course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.