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Last update: TAJ143 (03.12.2013)
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Last update: TAJ143 (03.12.2013)
Students will be able to:
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Last update: ROZ143 (02.08.2013)
R: Bergman N. H. (Ed.), Comparative Genomics (Volume 1 and Volume 2), Humana Press Inc. 2007, ISBN: 978-158829-693-1, 978-193411-537-4 R: Rodriguez-Ezpeleta N., Hackenberg M., Aransay A. M. (Eds.), Bioinformatics for High Throughput Sequencing, Springer Science 2012, ISBN: 978-1-4614-0781-2 A: Janitz M. (Ed.), Next-Generation Genome Sequencing: Towards Personalized Medicine, Wiley-VCH 2008, 978-3-527-32090-5 A: Brown S. M. (Ed.), Next-Generation DNA Sequencing Informatics, Cold Spring Harbor Laboratory Press 2012, ISBN: 978-1-936113-87-3 |
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Last update: ROZ143 (02.08.2013)
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Last update: ROZ143 (10.06.2013)
Zápočet: praktický projekt Zkouška: písemný test |
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Last update: ROZ143 (02.08.2013)
1. Itroduction to genomics and sequencing: historical overview, basic concepts. 2. Sequencing techniques: Sanger method, NGS (new generation sequencing): Illumina, SOLID, 454, etc. Comparison of sequencing techniques. 3. Sequencing data: Visualization - EnsEMBL, UCSC Browser, Artemis, ACT, Mummer, Circos. Base-calling and sequence quality control. Data formats. 4. DNA sequence assembly I: Sequence mapping onto reference genome. De novo assembly of long sequencies - newbler, mira. De novo assembly of short sequencies - WGS, velvet, soap2, AbySS. 5. DNA sequence assembly II: Sequencing projects, cDNA sequencing, scaffold formation. Software - Staden, AMOS, Consed. 6. Genome annotation: Prediction of gene models. Identification of non-coding RNA. Identification of protein domains. Functional annotation. Database sources and annotation systems. 7. Detection of sequence variations: Identification of single-nucleotide polymorphisms (SNPs), insertions and deletions, translocations, inversions, and copy-number variations (CNVs). 8. Analysis of protein-nucleic acid: ChIP-seq - protein/DNA interaction. CLIP-seq - protein/RNA interaction. 9. Differential expression I: RNA-seq. Sequence mapping. Measurement of gene expression. Normalization, summarization and differential expression. Identification of transcript variants - alternative splicing. Experimental design. 10. Differential expression II: micro RNA expression profiling. Identification of novel micro RNAs. 11. Epigenomics: Analysis of whole-genome methylation maps. 12. Metagenomics: gene annotation and metabolism reconstruction - MG-RAST. Amplicon sequencing (16S rDNA) and analysis of taxonomic units. 13. Comparative genomics: Interspecific genome comparison. 14. Genome projects: ENCODE. Paleogenomics. Sequencing projects. WWW tools - Galaxy, GMOD, Gbrowser, BioCycle, RAST, EnsEMBL API. Personalised medicine. |
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Last update: ROZ143 (02.08.2013)
Biochemistry, Molecular genetics |
Teaching methods | ||||
Activity | Credits | Hours | ||
Obhajoba individuálního projektu | 0.5 | 14 | ||
Účast na přednáškách | 1 | 28 | ||
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi | 1 | 28 | ||
Práce na individuálním projektu | 0.5 | 14 | ||
Příprava na zkoušku a její absolvování | 1 | 28 | ||
4 / 4 | 112 / 112 |
Coursework assessment | |
Form | Significance |
Defense of an individual project | 30 |
Examination test | 70 |