3577.16 - Bioinformatics in Practice
Bioinformatics in Practice
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 Cell and molecular biology I, 3516 Genetics, 3576 Cell and molecular biology II.
To provide the students with some theoretical and practical knowledge of bioinformatic tools for analyzing biological data.
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. Small molecules binding to proteins. NGS file formats. RNA Seq analyses. Genetic variation, haplotypes, GWAS, imputation, genetic diseases. Galaxy. Metagenomics and QIIME. Phylogeny and MEGA. Image analyses and Image J. Experimental design. Data privacy and ethics. Data life cycle and ecosystem.
Learning and teaching approaches
Lectures. Demonstrations. Problem solving. Discussions. It is strongly recommended that the students attend the lectures. The lectures may include access to external servers, installation of software, direct demonstrations, training sessions, exercizes, etc., and the lecturer may need the direct access to the students’ computers. Note that use of such installed programs and external servers may be a part of the exam, and that is the student’s own responsibility that the needed programs are installed on their computers.
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 3Dstructures 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. Analyze 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. Analyze RNA Seq reads using a pre-established pipeline. 11. Analyze 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. Utilize image analysis for qualitative or quantitative purposes. 13. Critically evaluate experimental design, statistical considerations, data privacy, data life cycle and ethics in planning.
Combination of 1) accepted obligatory exercises, presentations or other tasks given to the students and 2) graded written examination. Ad 1). Any obligatory tasks must be delivered within the specified deadlines, and they must be accepted (no grading) by the instructor. Ad 2). Six-hour written examination. All auxiliary materials allowed, including Internet. The students use their own laptops. The exam is individual; no communication is allowed between the students or with other individuals. The student may attend the ordinary exam before all obligatory tasks are accepted, but the grading will only be made valid upon acceptance of the obligatory tasks. A potential re-examination will only be held next time the course is given. The complete course must then be followed again, as the curriculum might be more or less revised.
The lectures and handouts from the lecturers define the curriculum. Some of the curriculum may be taken from Jonathan Pevsner (2015) Bioinformatics and Functional Genomics. 3ed. Wiley Blackwell. ISBN: 978-1-118-58178-0 Note that the book should be regarded as a supporting text, rather than a textbook.