spring 2020
KJE-3604 Bioinformatics: Microbial genomics and metagenomics - 10 ECTS
Course content
Bioinformatics is a combination of biological science and information technology used in analyzing and deriving conclusions from large data sets. This course introduces the students to bacterial genomics and metagenomics. Genome-scale sequencing projects have led to an explosion of genetic information (gene sequences) available for analysis. The student will learn how these sequences can lead to a much fuller understanding of many biological processes.
The aim is to provide a theoretical introduction of the topics, tools and current trends in bacterial genomics and metagenomics, followed by practical exercises using the methodology on Next generation sequence data. Major topics will include:
- Genome sequencing: Quality control of sequence data, sequence assembly, assembly evaluation and functional annotation
- Comparative genomics: Contrasting multiple genome sequences and visualization of results
- Transcriptomics (RNA-sequencing): Identification of differential expressed genes
- Whole genome phylogenetic analysis: Reconstruction of phylogeny based on complete genome sequences
- Metagenome sequencing: Preprocessing of raw sequence data and preparation for downstream sequence analysis
- Taxonomic classification of metagenomes: Taxonomic profiling of bacterial communities and comparison of profiles from different communities
Objectives of the course
The student will have acquired a solid and broad theoretical basis to understand bioinformatics. This means that the student
Knowledge
- has advanced knowledge in genomics and the analysis of this type of data including:
- quality control and assembly of sequence data
- evaluation of sequence assemblies
- functional annotation of DNA sequences
- RNA sequence analysis
- whole genome phylogeny
- taxonomic and functional profiling and binning of metagenomes
- has thorough knowledge of the scholarly or artistic theories and methods in the field
- can apply knowledge to new areas within the academic field
- can analyze academic problems on the basis of the history, traditions, distinctive character and place in society of the academic field
Skills
- can analyze and deal critically with various sources of information and use them to structure and formulate scholarly arguments
- can analyze existing theories, methods and interpretations in the of microbial genomics and metagenomics, and work independently on practical and theoretical problems
- can use relevant bioinformatical analysis methods for research and scholarly development work in an independent manner
- can carry out an independent, limited research or development project under supervision and in accordance with applicable norms for research ethics
Competence
- can analyze relevant academic, professional and research ethical problems
- can apply his/her knowledge and skills in new areas in order to carry out advanced assignments and projects
- can communicate extensive independent work and masters language and terminology used in the field of microbial genomics and metagenomics
- can communicate about academic issues, analyses and conclusions in the field of microbial genomics and metagenomics, both with specialists and the general public
- can contribute to new thinking and innovation processes
Recommended reading/syllabus
Pensumliste for KJE-3604 - Bioinformatics: Microbial genomics and metagenomics- About the course
- Campus: Tromsø |
- ECTS: 10
- Course code: KJE-3604
- Responsible unit
- Institutt for kjemi
- Kontaktpersoner
-
Erik Hjerde
Forsker, Molekylære biosystemer og bioinformatikk, Norstruct
+4777623372
erik.hjerde@uit.no -
Renate Lie Larsen
Seniorkonsulent, studieadministrasjon, Innkjøper Institutt for kjemi,
+4777644074
renate.larsen@uit.no
- Tidligere år og semester for dette emnet