BM121: Bioinformatics III: Biological Sequence Analysis (5 ECTS)

STADS: 0104041

Level


Teaching period

Autumn semester.

Teacher responsible
Email: lenem@imada.sdu.dk

Timetable
There is no timetable available for the chosen semester.

Comment:
Kurset undervises på engelsk, hvis internationale studerende deltager.
Skema aftales mellem de studerende og underviser.

Prerequisites:
None

Academic preconditions:
DM02 - Algorithms and Datastructures and ST05 or Science Statistics is recommended.

Course introduction
To provide students with a thorough understanding of the theory and computational techniques behind the most important algorithms in bioinformatics. The main emphasis will be put on sequence alignment and evolutionary trees.

Expected learning outcome


Subject overview
• Biology primer. A cursory overview of
• DNA
• The structure of genes in eukaryots and prokaryots
• Translatation and transcription
• Proteins

• Hidden Markov Models (HMMs)

• Sequence alignment
• Applications: similarity, homology searches, gene finding
• Score metrics
• ultrametric
• additive
• other (important examples are the PAM and Blosum matrices)
• Global alignment
• using dynamic programming
• using pair HMMs
• Local alignment
• Multiple alignment
• optimizing the sum of pairs score
• using a guide tree (an example is ClustalW)

• Evolutionary trees
• Character based methods: maximum parsimony
• Distance based methods
• UPGMA
• Neighbour joining
• Probabilistic approaches: introduction to
• maximum likelihood methods
• Bayesian methods

• Protein structure
• Predicting secondary structure using HMMs
• Overview of methods for predicting tertiary structure:
• Threading
• Simulation
• Comparative modeling
• Lattice models

• RNA structure


Literature

• R. Durbin, S. Eddy, A. Krogh, G. Mitchinson : Biological Sequence Analysis.
• Supplerende materiale udleveres . .

Syllabus
See syllabus.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
None

Assessment and marking:
A final project and two smaller assignments. The assignments are to be done individually, and the projects in groups of two-three students. The project can be either the implementation project or a literature study resulting in a report of five-ten pages. Internal evaluation (by instructor only). Pass / fail.

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

Forelæsninger (30 timer), øvelsestimer (5 timer), Vejledning (5 timer).
Educational activities

Language
No recorded information about the language used in the course.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.