Biological Sequence Analysis

Course content

The course covers the fundamental theoretical background for biological sequence analysis as well as applications of the methods, which are learned through homework and exercises. The topics include

  • Alignment methods for biological sequences (DNA, RNA, proteins)
  • Methods for searching sequence databases
  • Hidden Markov models with applications
  • Motif finding and discovery
  • Mapping and assembly of DNA sequencing data
  • The knowledge and skills acquired in this course will enable the students to understand and develop state-of-the-art algorithms.

MSc Programme in Biochemistry
MSc Programme in Bioinformatics
MSc Programme in Biology
MSc Programme in Biology with a minor subject
MSc Programme in Molecular Biomedicine

Learning outcome


The student will:

  • know the field of biological sequence analysis
  • know and understand the main algorithms and methods used in
    • pairwise and multiple alignment
    • searching of sequence databases
    • hidden Markov models of biological sequences
    • finding and discovery of motifs in biological sequences
    • mapping and assembly of DNA sequencing data
  • understand the biological contexts in which to apply biological sequence analysis


The student will be able to:

  • derive simple probabilistic methods and algorithms for biological sequence analysis
  • explain the algorithms and methods covered in the course
  • interpret results of standard methods used in biological sequence analysis
  • select the proper sequence analysis methods and tools for a given biological problem
  • run some standard computer programs for biological sequence analysis


The student will obtain these general competences:

  • Will be able to discuss and explain methods in biological sequence analysis with researchers in bioinformatics and related sciences
  • Will be able to contribute to interdisciplinary projects involving biological sequence analysis
  • Will be able to read, understand, and discuss scientific literature in biological sequence analysis

Lectures (4-5 per week), exercises (2-4 hours per week) and homework (one per week).

See Absalon.

Knowledge within molecular biology is recommended (can be obtained simultaneously). Programming at the level of "Linux and Python Programming" is recommended (can be taken simultaneously). Some skills in math and statistics are an advantage.

Academic qualifications equivalent to a BSc degree is recommended.

The course is mandatory in the bioinformatics graduate programme, but it is open to third year BSc-students and MSc-students in general. Participants are expected to bring a laptop equipped with a network card to class (contact teacher if not possible).

Feedback by final exam (In addition to the grade)
7,5 ECTS
Type of assessment
Oral examination, 30 minutes
Type of assessment details
Preparation time 30 minutes.
Written aids allowed

The use of Large Language Models (LLM)/Large Multimodal Models (LMM) – such as ChatGPT and GPT-4 – is permitted during the preparation time.

Marking scale
7-point grading scale
Censorship form
External censorship

The same as the ordinary exam.

Criteria for exam assessment

In order to obtain the grade 12 the student should convincingly and accurately demonstrate the knowledge, skills and competences described under Learning Outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 40
  • Preparation
  • 141
  • Practical exercises
  • 24
  • Exam
  • 1
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 1
The number of seats may be reduced in the late registration period
Study Board for the Biological Area
Contracting department
  • Department of Biology
Contracting faculty
  • Faculty of Science
Course Coordinator
  • Amelie Stein   (12-657169706d69327778696d7244666d73326f7932686f)
Saved on the 24-08-2023

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Courseinformation of students