KJE-2004 Bioinformatics - An introduction - 10 stp

Applicants from Nordic countries: Generell studiekompetanse eller realkompetanse + Matematikk R1 og R2 og enten Fysikk (1+2) eller Kjemi (1+2) eller Biologi (1+2) eller Informasjonsteknologi( 1+2) eller Geologi (1+2) eller Teknologi og forskningslære (1+2).

International applicants: Higher Education Entrance Qualification and certified language requirements in English. It is a requirement that students have  some prior knowledge of biology and ecology, chemistry and mathematics (Participants must have taken introductory level university courses, and achieved pass grades, in these subjects).

A list of the requirements for the Higher Education Entrance Qualification in Norway can be found on the Norwegian Agency for Quality Assurance in Education website - nokut.no

Application code: 9336 (Nordic applicants).

Knowledge:

The candidate

Background basics:

• has basic knowledge about DNA and RNA structure, the central dogma, gene structure and control, and the tree of life and evolution.
• has basic knowledge about primary and secondary protein structure, and implications for bioinformatics.

Biological databases:

• has insights into public databases, primary and secondary databases, file formats in bioinformatics and data quality.

Sequence alignments:

• knows the principals of sequence alignments.
• has knowledge about pairwise sequence alignments and database similarity searching (BLAST and FASTA).
• has knowledge about local and global alignments, and the dot-plot and dynamic programming methods.
• has knowledge about patterns, profiles and multiple sequence alignments (progressive alignment method, Clustal, T-Coffee, iterative methods).
• knows about protein motif and domain databases (Pfam, InterPro), and sequence logos.

Evolutionary processes:

• has background knowledge on mechanisms of mutations and evolutionary prodesses
• has background knowledge about principals for inferring phylogenies.
• has knowledge into basic principles of structure and interpretation of phylogenetic trees.
• has knowledge about how to reconstruct phylogenetic trees.

Next-generation DNA sequencing (NGS) and informatics:

• has knowledge about the history of DNA sequencing and its experimental applications.
• knows about early bioinformatics methods.
• has knowledge about how to visualize NGS data.

Genome characteristics:

• has knowledge about general genome features.
• knows how to predict genes, splice sites, promoters.
• has knowledge about detection of genes, introns/exons.

Skills:

The candidate

• can describe the basic properties of DNA,  RNA and protein. Explain the central dogma, and is able to outline structures and types of biological databases.
• can score alignments, use search tools, elaborate on substitution scoring matrices, dynamic programming, profiles and hidden Markov models.
• can carry out phylogenetic analyses using different methods, test resulting trees using the bootstrapping method, and interpret the result.
• is able to recognize typical gene features and assign function to genes (genome annotation).
• can elaborate on different DNA sequencing methods (Sanger and NGS methods).
• can outline applications of sequencing and expression profiling techniques .
• can present academic material

General competence:

The candidate

• understands the relation between DNA, RNA and protein, and can use this information to discuss their function.
• can participate in discussions concerning bioinformatics with others.
• has the ability to plan and execute basic bioinformatics tasks; aligning and handling sequences, database searching, phylogenetic analysis, and basic annotation.
• can interpret and communicate scientific material on bioinformatics.

The date for the exam can be changed. The final date will be announced at your faculty early in May and early in November.

New book: Concepts in bioinformatics and genomics, Eds. Momand & McCurdy, 2017, Oxford University Press

Contact the course responsible for more information. Details of the course are given through Canvas, the new learning portal of the university. You must be a registered student for the course in order to gain access to Canvas.