Kursussøgning, efter- og videreuddannelse – Københavns Universitet

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Kursussøgning, efter- og videreuddannelse

Biological Sequence Analysis

Practical information
Study year 2016/2017
Block 1
Programme level Full Degree Master
Course responsible
  • Anders Krogh (6-69737a776f70486a717736737d366c73)
  • Department of Biology
Course number: NBIA05008U

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

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

Recommended prerequisites

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.


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).

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  • MSc Programme in Bioinformatics
  • MSc Programme in Biology
  • MSc Programme in Molecular Biomedicine
  • MSc Programme in Biochemistry


Study Board of Biomolecular Sciences and Technology

Course type

Single subject courses (day)


1 block


---- SKEMA LINK ----

Teaching and learning methods

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






See Absalon.


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


Type of assessment

Oral examination, 30 minutes
Oral examination (30 minutes) with preparation time (30 minutes).

Marking scale

7-point grading scale

Criteria for exam assessment

In order to achieve the grade 12 the student must be able to demonstrate an excellent fulfillment of the learning outcome described above.

Censorship form

External censorship


Oral examination (30 minutes) with preparation time (30 minutes).

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