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Lecturer(s)
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Course content
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Nucleic acids and their structure. Sequence databases, sequence comparison, multiple alignment, tools for basic sequence analysis. Sequencing methods, base calling, sequencing errors. Sequence storage, file formats. Strategy to sequence eukaryotic genomes. Sequence assembly, graph-based algorithms, overlap-layout-consensus, de Bruijn graphs, basic assemblers. Visualization of assembled sequence. Genome annotation, repetitive DNA, genes, automated annotation, manual editing, tools and formats for genome annotation. Whole-genome visualization, databases to store completed genomes, GMOD, GBrowse. Genome-scale sequence comparison. Resequencing, read mapping to reference sequence. Genome variability in a population. Polymorphism identification, copy number variation, structural variation, single nucleotide polymorphism.
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming), Demonstration
- Preparation for the Exam
- 35 hours per semester
- Attendace
- 26 hours per semester
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Learning outcomes
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The course will introduce basic and advanced tools for analysis of DNA sequences. Students will learn to analyse large-scale data produced by next-generation sequencing technologies.
After the course, student should be able to: - assembly and annotate sequence of eukaryotic origin - perform large-scale sequence comparison (? Mb) - align sequence reads to reference genome and identify sequence polymorphism
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Prerequisites
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Successful completion of bachelor's level study requirements.
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Assessment methods and criteria
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Written exam, Student performance
Written test - 75% correctly answered questions; 80% attendance; completion of seminar project.
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Recommended literature
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Cvrčková, F. (2006). Úvod do praktické bioinformatiky. Academia, Praha.
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Mount D.V. (2004). Bioinformatics. Sequence and Genome Analysis. New York.
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