Course title | Bioinformatics for Biologists |
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Course code | KMB/615 |
Organizational form of instruction | Lecture + Lesson |
Level of course | Master |
Year of study | not specified |
Frequency of the course | In academic years starting with an odd year (e.g. 2017/2018), in the summer semester. |
Semester | Summer |
Number of ECTS credits | 6 |
Language of instruction | Czech |
Status of course | Compulsory-optional |
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 |
Content of lectures: 1. What is bioinformatics, typical bioinformatics problems, types of biological data, introduction to databases 2. Databases, database structure, most important databases of biological information and online services, NCBI, EMBL-EBI, ELIXIR infrastructure 3. DNA and protein sequences, sequence alignment, pairwise and multiple alignment 4. Position specific substitution matrices, profiles, hidden Markov models, PSI-BLAST 5. NCBI blast, searching sequence databases 6. DNA sequencing, assembly, genome assembly, contig, scaffold, next generation sequencing 7. Genome architecture and evolution, genome annotation, gene prediction, comparative genomics 8. Gene expression analysis, microarrays, RNA-Seq, ChiP-Seq, EST 9. Gene ontologies, signal pathways 10. Molecular phylogenetics 11. "omics" data, high throughput technologies, processing of "big data", algorithms for clustering 12. Structural bioinformatics: protein structure analysis - protein surface, charge, conserved residue, motifs, protein function prediction 13. Structural bioinformatics: prediction of 3D structure, ab initio prediction, homology modelling, protein structure databases 14. Molecular interaction, docking, virtual screening, drug design and discovery Content of practicals: Student will learn how to uses methods introduced in lectures
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Learning activities and teaching methods |
Monologic (reading, lecture, briefing), Demonstration, Laboratory, E-learning
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Learning outcomes |
The aim of this course is to introduce students with specialization in biology to the new field of bioinformatics. Students will learn about basic algorithms and tools for analysis of data in biology, how to use databases and bioinformatics software.
Students will understand how to process, analyze, and interpret data from molecular biology experiments, how to obtain and use data from biological databases. |
Prerequisites |
Understanding of molecular biology and genetics KMB/023 KMB/250
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Assessment methods and criteria |
Oral examination, Analysis of student's work activities (technical works), Test
Requirements for credit: 1) presence on the practical trainings (maximum one absence) 2) submission ofresults from each practical training assignment 3) successful passing of final test (Students must achieve at least 50% score) Requirements for oral exam: 1) obtaining of the credit |
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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Faculty: Faculty of Science | Study plan (Version): Experimental Biology (1) | Category: Biology courses | - | Recommended year of study:-, Recommended semester: - |