Syllabus for Methods in Bioinformatics

Bioinformatisk metodik

Syllabus

  • 5 credits
  • Course code: 1MB331
  • Education cycle: First cycle
  • Main field(s) of study and in-depth level: Biology G2F, Technology G2F, Chemistry G2F

    Explanation of codes

    The code indicates the education cycle and in-depth level of the course in relation to other courses within the same main field of study according to the requirements for general degrees:

    First cycle
    G1N: has only upper-secondary level entry requirements
    G1F: has less than 60 credits in first-cycle course/s as entry requirements
    G1E: contains specially designed degree project for Higher Education Diploma
    G2F: has at least 60 credits in first-cycle course/s as entry requirements
    G2E: has at least 60 credits in first-cycle course/s as entry requirements, contains degree project for Bachelor of Arts/Bachelor of Science
    GXX: in-depth level of the course cannot be classified.

    Second cycle
    A1N: has only first-cycle course/s as entry requirements
    A1F: has second-cycle course/s as entry requirements
    A1E: contains degree project for Master of Arts/Master of Science (60 credits)
    A2E: contains degree project for Master of Arts/Master of Science (120 credits)
    AXX: in-depth level of the course cannot be classified.

  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2009-03-16
  • Established by:
  • Revised: 2018-08-30
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 30, 2019
  • Entry requirements: 60 credits within the programme including Structural Bioinformatics, and Probability and Statistics. Completed Database Design I and Programming Techniques II.
  • Responsible department: Biology Education Centre

Learning outcomes

On completion of the course, the student should be able to:

  • explain the principles of sequence alignments, pattern recognition and phylogenetic analysis
  • construct bioinformatic workflows and use scripts for data management
  • solve given biological problems by identifying and using the appropriate public databases, and choose and apply existing software
  • analyse, evaluate and compile results of bioinformatic analyses critically

Content

The course mainly deals with bioinformatics with focus on sequence data and contains the following parts and aspects:

Public bioinformatic databases, their design and search tools. Identification of coding sequences. Pair-wise and multiple sequence alignment, heuristic methods for sequence alignment. Automation of bioinformatic analyses by means of script programming. Models for sequence evolution and statistical sequence comparisons. Methods for phylogenetic analysis and pattern recognition.

Instruction

The course consists of lectures and computer exercises.

Assessment

Parts of the course: Theory 2 credits; computer exercises 3 credits.

For the overall grade Pass, it is required that the computer exercises have been presented in writing and orally and are passed. The theory part is examined in a written examination. 
 
If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.

Reading list

Reading list

Applies from: week 30, 2019

  • Zvelebil, Marketa J.; Baum, Jeremy O. Understanding bioinformatics

    New York: Garland Science, c2008

    Find in the library

    Mandatory