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Lecturer(s)
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Symonová Radka, doc. Mgr. Ph.D.
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Course content
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1. Work with sequences in formats FASTA and FASTQ 2. Complementary sequences, reverse and reverse complement, motifs search 3. DNA sequence similarity assessment and BLAST 3. Genomic data, calculations of GC% at levels of DNA, cDNA and cds and compared with fragments length, GC1/2/3 in cds, CpG search 5. Nucleotide databases and work with them (Ensembl, ENA, NCBI, API/Entrez) 6. Construction of phylogenetic trees based on DNA sequences 7. Pairwise and multiple sequence alignment 8. Gene prediction, codon analysis, codon adaptation index 9.-10. Ad hoc bioinformatics tools using Python and Biopython Practical work with DNA sequences according to the topics of each lecture.
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Learning activities and teaching methods
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- Preparation for classes
- 25 hours per semester
- Preparation for exam
- 25 hours per semester
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Learning outcomes
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The goal of the course is to learn using Python/Biopython and other accessible tools for basic bioinformatical analysis. From training and common semestral project, the students will gain the survey of existing possibilities and practical experience.
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Prerequisites
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UAI 735I Python Basics
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Assessment methods and criteria
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unspecified
The semestral project comprises students' own analysis together with detailed documentation.
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Recommended literature
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Antao T. Bioinformatics with Python, Cookbook.
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Jones M. 2013. Python for Biologists.
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Jones M. 2014. Advanced Python for Biologists.
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Jones M. 2016. Effective Python Development for Biologists.
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Jones M. 2020. Biological Data Exploration with Python, Pandas and Seaborn.
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Matoulek et al. 2021. GC and Repeats Profiling along Chromosomes-The Future of Fish Compositional Cytogenomics https://www.mdpi.com/2073-4425/12/1/50.
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Stevens & Boucher. 2015. Python Programming for Biology. Cambridge.
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www.biopython.org.
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