3577 - Bioinformatics in Practice
Course information
- Title
- Bioinformatics in Practice
- Course number
- 3577.24
- Academic year
- 2024-2025
- ECTS
- 7.50
- Level
- Bachelor
- Faculties
- Science and Tecnology
- Educations
- BSc in Molecular Life Sciences
- Prerequisites
- A) Admitted to the bachelor programme in biology at the University of the Faroe Islands, and following the normal study progression or B) Students following single courses need to have sufficient background in molecular courses, like 3514 Biochemistry, 3518 Molecular cell biology I, 3516 Genetics, 3576 Molecular cell biology II
- Language of instruction
- The course is taught in English, Danish, Norwegian and Faroese. Instructional materials are in English.
- Registration
- Students on the fifth semester of B.Sc. in Molecular Life Sciences are automatically enrolled. Applicants for an individual course must apply via the Student Service Center at lss@setur.fo
- Beginning date
- Monday, October 28, 2024
- End date
- Thursday, December 19, 2024
Academic content
- Purpose
- To provide the students with some theoretical and practical knowledge of bioinformatic tools for analysing biological data.
- Learning outcomes
- On completion of the course, the successful student should be able to: 1. Describe principles of sequence alignments and how sequence alignments can be used for different purposes. 2. Critically evaluate results from sequence alignments. 3. Search in and extract data from different public sequence and structure databanks, like GenBank, UniProt, Ensembl, PDB, etc. 4. Describe the purposes for and needs of annotation, and use some of the tools for such annotation, in particular Gene Ontology (GO). 5. Visualize, manipulate and model 3D structures of proteins, and describe interactions of small molecules with 3D models. 6. Manually determine the sequence of a simple peptide MS/MS spectrum, and identify which protein this peptide comes from. 7. Analyse MS (MALDI) and MS/MS peptide spectra using web-based tools to identify and quantify proteins and post-translational protein modifications. 8. Describe both positive and negative consequences of genetic variations, and indicate how such variations can be detected. 9. Comprehend and describe the principles of targeted (16S rRNA or other genes) or untargeted metagenomics. 10. Describe some central principles in assembly of sequences (whether transcriptome, genome or other large-scale sequence data) from modern sequencing technologies. 11. Analyse evolutionary relationships: (i) by describing how DNA and protein sequences can be used to indicate the evolution of gene families and related species, and (ii) by actually performing phylogenetic analyses, starting from one or a few related sequences. 12. Critically evaluate experimental design, statistical considerations, data privacy, data life cycle and ethics in planning.
- Content
- Brief introduction to NGS techniques and different large-scale sequencing targets (genome, exome, RNA Seq, etc). Sequence alignments. Databases and searches in databases. Protein identification/modification/quantitation bioinformatics. Functional analyses and Gene Ontology. Biostatistics and R. Structural (3D) bioinformatics of proteins. Genetic variation, haplotypes, GWAS, imputation, genetic diseases. Metagenomics and QIIME. Phylogeny and MEGA. Experimental design. Data privacy and ethics. Data life cycle and ecosystem.
- Learning and teaching approaches
- Lectures, demonstrations, workshops, problem solving, and discussions.
Assessment
- Assessment method
- Combination of 1) workshop exercises and 2) poster presentation. Ad 1). All mandatory workshop exercises must be completed and accepted before the poster presentation (grade will not be given for this part). Once this part has been accepted, it is also valid in case of re-examination. Ad 2). The students must make a poster presenting results from a selected workshop and present this poster in a poster session (grade will be given for this part).
- Examination (internal/external)
- Internal
- Grading scale
- 7-scale
- Exam date/dates
- The combined assessment is set for 19th of December, 2024
- Deadline for withdrawal from exam
- Monday, October 28, 2024
Academic responsibility and teachers
- Academic responsibility
- Sunnvør Klettskarð í Kongsstovu
- Teachers
- Sunnvør Klettskarð í Kongsstovu, Svein-Ole Mikalsen, Anni Djurhuus, Bent Petersen, Henrik Nielsen