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