autumn 2019

KJE-2004 Bioinformatics - An introduction - 10 ECTS

Sist endret: 31.10.2019

The course is provided by

Faculty of Science and Technology

Location

Tromsø |

Application deadline

Applicants from Nordic countries: 1 June for the autumn semester 

Exchange students and Fulbright students: 15 April for the autumn semester.

Type of course

Theoretical and practical subject. The course is available as a singular or elective course independent of study program, also to exchange students. The course is offered on condition that a minimum number of students register for the course.

Admission requirements

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: 9336 (Nordic applicants).

Course content

With the recent revolution in our biological understanding and available data, and the rapid development of new technologies, it is today expected that modern biologists are competent in using bioinformatics tools. This course introduces students to Bioinformatics and Bioinformatics tools, and provides participants with hands-on training. Students will be introduced to biological sequence data (DNA and protein sequences, whole genomes, learn to access major sequence databases and use a variety of web-based services. During the course, the students will learn to retrieve, analyze, compare and visualize genetic sequences.

Objectives of the course

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

Language of instruction

The language of instruction is English and all of the syllabus material is in English. Reports may be written in English or a Scandinavian language.

Teaching methods

Lectures: 27 h, Laboratory: 24 h PC-based exercises.

Assessment

A 4 hour final written exam counting 100%. Letter grades A-E, F - fail. 

Work requirement: Approved project reports. Mandatory attendance in laboratory exercises.

Students who have not passed the last ordinary exam can re-sit the written exam early the following semester.

Date for examination

Written examination 04.12.2019

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

Schedule

Course overlap

BIO-2304 Introduction to Bioinformatics 10 stp


Kontakt
Profilbilde Renate Lie Larsen

Renate Lie Larsen


Seniorkonsulent, studieadministrasjon, Innkjøper institutt for kjemi,
Telefon: +4777644074 renate.larsen@uit.no

Peik Haugen.jpg

Haugen, Peik


Professor, Molekylære biosystemer, Norstruct
Telefon: +4777645288
Mobil: 95122932 peik.haugen@uit.no