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: The Faculty Board of Science and Technology
  • Applies from: week 27, 2007
  • Entry requirements: Bachelor's degree including alternative 1) 40 credit points/60 credits biology and 20 credit points/30 credits chemistry or 20 credit points/30 credits earth sciences; alternative 2) 60 credit points/90 credits 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

Reading list

Applies from: week 27, 2007

Some titles may be available electronically through the University library.