KJE-2004 Bioinformatics - An introduction - 10 stp

Applicants from Nordic countries: KJE-1001 or equivalent

International applicants: Higher Education Entrance Qualification and certified language requirements in English. It is a requirement that students have some prior knowledge of chemistry and/or biology (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: 9197 (Nordic applicants).

The student will have basic knowledge and proficiency within bioinformatics. This means that the student

Knowledge

Background basics

• has basic knowledge about DNA and RNA structure, the flow of genetic information in cells (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 principles behind sequence alignments
• has knowledge about pairwise sequence alignments and database similarity searching (BLAST)
• 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, iterative methods)
• knows about protein motif and domain databases (Pfam, InterPro), and sequence logos

Protein structure prediction

• has background knowledge into how secondary and tertiary protein structure are determined, and how bioinformatics tools can be used to visualize such structures

Evolutionary processes

• has background knowledge on mechanisms of mutations, natural selection and evolutionary processes
• has background knowledge about the molecular clock assumption and other principals for inferring phylogenies
• has knowledge into basic principles of structure and interpretation of phylogenetic trees

• has knowledge about how to reconstruct phylogenetic trees

Genomics

• has knowledge about DNA sequencing and its experimental applications
• has knowledge about general genome features
• knows how to predict genes, promoters, terminators
• has knowledge about detection of genes

Skills

• can describe the basic properties of DNA, RNA and protein
• can explain the general flow of genetic information in cells (central dogma), and is able to outline the types of biological databases, and their general content.
• can describe how protein structures can be predicted
• can score alignments, use search tools, elaborate on substitution scoring matrices, dynamic programming, and sequence profiles (position specific scoring matrices)
• can carry out phylogenetic analyses using different methods, test resulting trees using the bootstrapping method, and interpret the result
• can recognize typical gene features and assign function to genes (genome annotation)
• can elaborate on polymerase chain reaction (PCR), different DNA sequencing methods (Sanger and NGS methods), and the human genome
• can outline applications of sequencing and expression profiling techniques
• can present academic materials

Competence

• 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, protein structure prediction, phylogenetic analysis, and basic annotation and programming
• 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.