Master’s studies

Syllabus for Bioinformatic Analyses I

Bioinformatiska analyser I

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), 3, 4, 5.
  • Established: 2007-03-15
  • Established by: The Faculty Board of Science and Technology
  • Revised: 2011-11-23
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 27, 2012
  • 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. After the course, the student shall 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.

Reading list

Applies from: week 27, 2012

  • Xiong, Jin Essential bioinformatics

    New York: Cambridge University Press, 2006

    Find in the library