| Course title | Practical Bioinformatics |
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| Course code | KBC/PGPB |
| Organizational form of instruction | Lecture |
| Level of course | Doctoral |
| Year of study | not specified |
| Semester | Winter and summer |
| Number of ECTS credits | 5 |
| Language of instruction | Czech, English |
| Status of course | unspecified |
| Form of instruction | Face-to-face |
| Work placements | This is not an internship |
| Recommended optional programme components | None |
| Lecturer(s) |
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| Course content |
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Biological databases - sequence databases; specialized databases of biomolecules (e.g. proteolytic enzymes, restriction endonucleases etc.); data formats in databases; obtaining information from biological databases; preparation of custom databases. Working with protein and nucleic acid sequences - sequence-based prediction of spatial structure, properties and function of biomolecules; multiple sequence alignment; sequence logo; prediction of gene introns and nucleotide polymorphisms. Molecular phylogenetics - gene orthologs and paralogs; phylogenetic tree design - distance- and character-based methods, phylogenetic software; visualization of phylogenetic trees. Genomics and proteomics - assembling of genomic sequences; functional genomics; identification and quantification of proteins in the sample; analysis and prediction of posttranslational modifications and protein-protein interactions. Glycomics - structure and diversity of carbohydrates; database of carbohydrates and glycoenzymes; experimental analysis of glycans and glycoproteins; software for glycosylation prediction and interpretation of glycomics data; protein-carbohydrate interaction and its analysis. Other topics for bioinformatics in biochemistry - image analysis (electrophoresis); analyzing chromatographic and mass spectrometry data; manual interpretation of tandem mass spectra of peptides and oligonucleotides; data analysis from enzyme kinetics; MALDI mass spectrometry of microorganisms and its use for phylogenetics.
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| Learning activities and teaching methods |
| Dialogic Lecture (Discussion, Dialog, Brainstorming) |
| Learning outcomes |
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Biological databases, working with protein and nucleic acid sequences, molecular phylogenetics, genomics and proteomics, glycomics, other topics for bioinformatics in biochemistry.
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| Prerequisites |
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Successful graduated studium of Bachelor of Science and Magister of Science in Biochemistry.
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| Assessment methods and criteria |
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Oral exam
Oral examination - successfuly answered three questions of general knowledge. |
| Recommended literature |
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| Study plans that include the course |
| Faculty | Study plan (Version) | Category of Branch/Specialization | Recommended semester |
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