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Lecturer(s)
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Šafářová Dana, Mgr. Ph.D.
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Course content
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Introduction to bioinformatics. Information sources, biologic databases (primary, secondary and specialized DB). Sequencing and commonly used strategies. Pairwise sequence alignment, database similarity searching. Multi-sequence alignment. Global and local alignment. Scoring matrices. Dynamic, heuristic and statistic approaches (PSSM, HMM). Gene prediction, ab initio and homology approach. Analysis of RNA. Analysis and structure prediction of proteins. Molecular phylogenetics, construction of phylogenetic trees. Genome analysis. Seminary: Practical applications of basic bioinformatic approach: databases (GenBank/NCBI, DDBJ, EBI, ENTREZ,), homology searching (BLAST, FASTA), single sequence alignment, multiple sequence alignment, phylogenetic analysis (CLUSTAL, MEGA, e-nástroje). Specialised software.
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Learning activities and teaching methods
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Lecture, Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming), Demonstration, Laboratory Work
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Learning outcomes
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Introduction into bioinformatics, basic analysis of data on DNA, RNA and protein level.
Student is able to (after attending the course): - Define the information sources, biologic databases - Explain the sequencing procedures and commonly used strategies sequence data analysis. - Explain procedures in gene prediction, ab initio and homology approach - Describe the procedures in analysis of RNA and analysis and structure prediction of proteins - Define the approaches in molecular phylogenetics, construction of phylogenetic trees - Recall the whole Genome analysis techniques.
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Prerequisites
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unspecified
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Assessment methods and criteria
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Written exam, Student performance
attendance, working out the practical tasks, test
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Recommended literature
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NCBI.
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Cvrčková F. Úvod do praktické bioinformatiky. Academia, Praha, 2006.
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Jin Xiong. (2006). Essential Bioinformatics. Cambridge.
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Mount D.V. (2004). Bioinformatics. Sequence and Genome Analysis. New York.
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Rashidi, H.H., Buehler, L.K. Bioinformatics Basics. CRC Press, Boca Raton, 2000..
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