Applied Bioinformatics

Undergraduate course

Course description

Objectives and Content

The course provides an introduction to the use of bioinformatics tools, including retrieval of information from databases, pairwise and multiple sequence alignments, phylogenetic trees,  analysis of protein structures, recognition of sequence patterns, as well as an introduction to the use of Python and Unix for bioinformatics analyses. The theoretical basis for selected methods, such as dynamic programming, is studied in detail. The course consists of lectures, exercises and group work.

Learning Outcomes

On completion of the course the student should have the following learning outcomes defined in terms of knowledge, skills and general competence:



  • The student has knowledge about which type of data is available from the most common protein sequence and structure databases (UniProt, GenBank, Protein Data Bank).
  • The student knows the theories underlying the most common methods for sequence searches and sequence alignments, and in particular knows the principle and main steps for pairwise and multiple sequence alignments;
  • The student can explain and is able to apply the main steps of dynamic programing for/to simple alignments of short sequences;
  • The student can explain the principles behind reconstruction and interpretation of phylogenetic trees;
  • The student understands connections between sequence similarity, 3D structure and function (for proteins), and evolutionary distance. 
  • Understands the principles of how 'Hidden Markow Models' and 'Position Specific Scoring Matrices' can be used of sequence pattern recognition.
  • The student knows about computational methods that can be used for the prediction of  protein 3D structure from sequence information.
  • The student has a basic understanding for how to use Unix and Python to analyse biological data.



The student is able to:

  • select and apply the most appropriate bioinformatics sequence or structure database to retrieve or search data given a specific question in molecular biology;
  • select and apply the most appropriate method for aligning sequences, reconstructing evolutionary relationships, visualizing and analyzing protein structures.
  • use python and unix to do simple bioinformatic analyses

General competence

  • The student is able to reflect using its knowledge and skills in bioinformatics so as to decide whether a given molecular biology problem could benefit from a bioinformatics approach, and which methods to use.
  • Using their theoretical knowledge about the most commonly used bioinformatics methods, the student is able, if encountering a new online tool, to get a general understanding of its underlying principle

ECTS Credits


Level of Study


Semester of Instruction


This course has a limited capacity, enrolment is based on application. The application deadline is Wednesday in week 3 for the spring semester. Please see this page for more information. You will receive confirmation of whether you received a seat in Studentweb no later than Monday the week after the deadline.

It is compulsory to attend the first lecture/orientation meeting, or you risk losing your seat. If you are unable to attend the first lecture, you must contact the Study Section ( The time of the first lecture/orientation meeting can be found in the schedule on the course website or on Mitt UiB.

Place of Instruction

Required Previous Knowledge
Recommended Previous Knowledge
Credit Reduction due to Course Overlap
BINF100: 5 ECTS,
Teaching and learning methods

The course is given as lectures and mandatory exercises

Lectures, 2 hours per week

Exercises, 4 hours per week

Compulsory Assignments and Attendance

The first lecture/orientation meeting is compulsory.

Towards the end of the semester a report centered about a set of bioinformatics problems must be submitted. The report must be approved before you can take the exam.

Completed activities are valid for 6 semesters (the current semester and the five following semesters). All mandatory activity must be approved before you can take the exam.

Forms of Assessment
Written exam, 4 hours.
Grading Scale
The grading scale used is A to F. Grade A is the highest passing grade in the grading scale, grade F is a fail.
Assessment Semester
An exam will be available each semester.
Reading List
The reading list will be available within July 1st for the autumn semester and December 1st for the spring semester.
Course Evaluation
Students will evaluate the teaching in line with UiB and the Department's quality assurance system.
Examination Support Material
Non- programmable calculator, according to model listed in faculty regulations.
Programme Committee
The Programme Bard is responsible for the content, structure and quality of the study programme and courses.
Course Administrator
The Mathematics and Natural Sciences - Department of Biological Sciences has the responsibility for the course and programme.