SubjectsSubjects(version: 853)
Course, academic year 2019/2020
  
Genomics: algorithms and analysis - M143003
Title: Genomika: algoritmy a analýza
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: winter
Points: winter s.:4
E-Credits: winter s.:4
Examination process: winter s.:
Hours per week, examination: winter s.:2/1 C+Ex [hours/week]
Capacity: unlimited / unlimited (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Pačes Jan Mgr. Ph.D.
Interchangeability : N143046
Annotation -
Last update: Hladíková Jana (04.01.2018)
Within this course contemporary high-throughput sequencing techniques are introduced. The main focus of the course is on individual applications such as, e.g., ChIP-Seq, RNA-Seq, resequencing, metagenomics or de-novo sequencing. A procedures of the complete analyses for individual applications will be described, and will be demonstrated during practical exercises. Explained knowledge includes sequence quality reading ("base calling") and its control, data formats and standards, advanced software tools and evaluation of their suitability, mapping of sequence data, short and long sequence assembly, identification of SNPs, and functional annotation.
Aim of the course -
Last update: Hladíková Jana (04.01.2018)

Students will be able to:

  • Know basic principles of contemporary sequencing techniques and their applications.
  • Will be acquainted with a branch terminology.
  • Will be able to analyse genomic data produced by experimental departments.
  • Will understand data formats, genomic data storage, assembly of short and long sequencies, sequence mapping onto known genomes.
  • Will be able to choose a suitable application to solve a given problem. Will gain general knowledge of existing software tools, their limitations and their strengths.
Literature -
Last update: Svozil Daniel doc. Mgr. Ph.D. (04.11.2018)

R: Martínková N., Analýza genomických a proteomických dat, Institut biostatistiky a analýz MU Brno, 2018, http://portal.matematickabiologie.cz/index.php?pg=analyza-genomickych-a-proteomickych-dat

R: Nosek J. a kol., Genomika (slovenská edice), CreateSpace Independent Publishing Platform, 2013, ISBN: 1494230623

R: Brown S. M. (Ed.), Next-Generation DNA Sequencing Informatics, Cold Spring Harbor Laboratory Press 2015, ISBN: 978-1621821236

A: Snustad, D. P., Simmons, M. J. Genetika. Nakladatelství Masarykovy univerzity, Brno, 2009, ISBN: 978-80-210-4852-2

A: Bergman N. H. (Ed.), Comparative Genomics (Volume 1 and Volume 2), Humana Press Inc. 2011, ISBN: 978-1617377228, 978-1617379338

A: 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

Learning resources -
Last update: Hladíková Jana (04.01.2018)

none

Requirements to the exam - Czech
Last update: Hladíková Jana (04.01.2018)

Zápočet: praktický projekt

Zkouška: písemný test

Syllabus -
Last update: Hladíková Jana (04.01.2018)

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.

Registration requirements -
Last update: Hladíková Jana (04.01.2018)

Biochemistry, Molecular genetics

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (29.01.2018)

A credit will be given based on assigmments during exercises and a seminar work. An exam consists of both oral and written parts.

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

 
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