Syllabus for Bioinformatic Analyses I

Bioinformatiska analyser I

A revised version of the syllabus is available.

Syllabus

  • 5 credits
  • Course code: 1BG311
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Biology A1N, Technology A1N
  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2007-03-15
  • Established by:
  • Revised: 2018-08-30
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 30, 2019
  • Entry requirements: 120 credits including (1) 60 credits in biology and 30 credits in chemistry or 30 credits in earth science, or (2) 90 credits in biology.
  • Responsible department: Biology Education Centre

Learning outcomes

The course focuses on comparative sequence analyses and public databases. On completion of the course, the student should be able to:

  • identify and choose appropriate public databases to solve a given biological problem
  • explain the principles for cost based sequence alignment
  • outline the process from sequence data to an annotated genome and explain the different techniques
  • that are used
  • choose and apply (for the problem area) existing software on given biological problems
  • implement simpler algorithms for data handling in Perl
  • critically analyse, evaluate and compile received results
  • Contents

Content

The course deals mainly with bioinformatics with focus on sequence data (DNA/RNA and protein) and contains the following parts and aspects:

Public bioinformatic databases, their design and search tools. Contig assembly. Identification of coding sequences. Pair-wise and multiple sequence alignment, heuristic methods for sequence alignment. Annotation of genomes.

Bioinformatic software and Linux environment. Automation of bioinformatic analyses using Perl.

Modules: Theory 2 credits; computer exercises 2 credits; projects 1 credit

Instruction

The teaching is given in the form of computer-based net teaching, lectures, computer exercises and project assignment.

Assessment

To pass the course is required that all computer exercises equivalent to 2 credits and project assignment equivalent to 1 credit has been presented in writing and is passed. The theory part is examined by a written examination equivalent to 2 credits.

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

Some titles may be available electronically through the University library.

  • Xiong, Jin Essential bioinformatics

    New York: Cambridge University Press, 2006

    Find in the library