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), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2007-03-15
  • Established by:
  • Revised: 2020-02-18
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 27, 2020
  • 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.
    English language proficiency that corresponds to English studies at upper secondary (high school) level in Sweden ("English 6").
  • 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
  • perform and evaluate pairwise and multiple sequence alignment
  • outline the process from sequence data to an annotated genome and explain the principles behind the different steps
  • perform basic annotation
  • manage basic commands in a Unix environment
  • choose and apply (for the problem area) existing software on given biological problems
  • critically analyse, evaluate and compile received results

Content

The course covers basic bioinformatics with focus on microbial genomic sequencing data and contains the following parts and aspects:

Next generation sequencing revolution. Examples of big sequencing projects. Storing and organising biological data. Public bioinformatic databases, their design and search tools.

Homology and sequence similarity. 'Nothing in biology makes sense except in the light of evolution' (Dobzhansky 1973) in a molecular context.

Principles for cost based pairwise sequence alignment. Heuristic methods (BLAST). Multiple sequence alignments - simple algorithm overview, guide tree concept.

Genome annotation workflow: sequencing, assembly, structural and functional annotation, comparative genomics. Basic theoretical concepts for identification of coding sequences. Sequence motifs. Examples from prokaryotic/eukaryotic microbial genomes. Phylogenetic framework in comparative genomics. Examples of biological questions addressed with genomics.

Principles of phylogenetics and examples of biological questions addressed with phylogenetics. Phylogenetic workflow overview.

Bioinformatic software and Linux environment. Automation of bioinformatic analyses using a scripting language.

Instruction

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

Assessment

Modules: Computer exercises 2 credits; projects 1 credit; theory 2 credits.
To pass the course is required that all computer exercises and project assignment has been presented in writing and is passed. The theory part is examined by 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 27, 2020

  • Xiong, Jin Essential bioinformatics

    New York: Cambridge University Press, 2006

    Find in the library