E7492 DNA Sequence Analysis

Faculty of Science
Autumn 2025
Extent and Intensity
2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
In-person direct teaching
Teacher(s)
doc. Mgr. Natália Martínková, Ph.D. (lecturer)
Guaranteed by
doc. Mgr. Natália Martínková, Ph.D.
RECETOX – Faculty of Science
Contact Person: doc. Mgr. Natália Martínková, Ph.D.
Supplier department: RECETOX – Faculty of Science
Timetable
Fri 8:00–10:50 F01B1/709
Prerequisites
Students are expected to understand the basic principles of molecular biology and genetics. For practical tasks, they will need an active Metacentrum account, which can be created at https://metavo.metacentrum.cz/cs/application/index.html.
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 12/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30
Course objectives
The goal of the course is to teach students how to assemble DNA sequences, understand the structure and use of genetic databases, evaluate DNA sequences, and identify them in a biodiversity context using phylogenetic analyses.
Learning outcomes
After completing the course, the student will be able:
- to formulate and test a hypothesis;
- to map sequencing reads to a reference;
- to use information from genetic databases;
- to identify an unknown sequence by searching genetic databases and comparing hits with suitable BLAST algorithms;
- to evaluate sequence identification;
- to calculate genetic distances using an appropriate substitution model;
- to reconstruct phylogenetic trees with distance methods, maximum parsimony, maximum likelihood, and Bayesian inference;
- to interpret phylogenetic relationships in a sequence dataset and critically assess conflicting results.
Syllabus
  • 1. Genomics: (a) Genomes, genome organisation, variability, (b) Genome sequencing – next-generation sequencing, pyrosequencing, sequencing by ligation.
  • 2. Genome assembly: (a) De novo assembly, resequencing, mutation detection, (b) Contigs – length and number, (c) Assembly parameters, (d) Coverage and variability detection.
  • 3. Sequence search: (a) GenBank, EMBL, DDBJ, UniProt, (b) Entrez, SRS, (c) Libraries and cross-referencing.
  • 4. BLAST: (a) Nucleotide BLAST, protein BLAST, megablast, PSI-BLAST, (b) Search principles, (c) Result evaluation and E-values.
  • 5. Genomic sequence annotation: (a) RNA prediction, (b) Genomic islands, (c) Protein prediction – prokaryotes.
  • 6. Genomic sequence annotation: (a) Protein prediction – eukaryotes, (b) CpG islands, (c) Annotation reports.
  • 7. Alignment: (a) Homologous positions, (b) Local and global alignment – assembly options, (c) Dynamic programming.
  • 8. Relationship modelling: (a) Phylogenetic tree terminology and interpretation, (b) Tree comparison.
  • 9. Substitution models: (a) Genetic distances, (b) Model parameters, (c) Problems and solutions.
  • 10. Phylogenetics: (a) Phylogenetic analyses – neighbour-joining, maximum parsimony, (b) Significance of signal and bootstrap support.
  • 11. Maximum likelihood: (a) Likelihood function, (b) Randomised accelerated maximum likelihood.
  • 12. Bayesian analysis: (a) Posterior probabilities, (b) Effect of priors on posterior distributions, (c) Convergence and Metropolis-coupled MCMC.
  • 13. Gene and species evolution: (a) Supermatrices, (b) Supertrees, (c) Bayesian estimation of species trees.
  • 14. Visualisation.
Literature
  • FELSENSTEIN, Joseph. Inferring phylogenies. Sunderland, Mass.: Sinauer Associates, 2004, xx, 664. ISBN 0878931775. info
  • CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Vyd. 1. Praha: Academia, 2006, 148 s. ISBN 8020013601. info
  • ZIMA, Jan. Genetické metody v zoologii. 1. vyd. Praha: Karolinum, 2004, 239 s. ISBN 8024607956. info
Teaching methods
Lectures, discussions, in-class data analysis, and homework focused on final project design.
Assessment methods
Five-minute tests throughout the course, a final project based on the student’s design, verbal interpretation of the project at the final exam, and a final written test. The project design must be submitted by 30 November, with the project analysis results presented at the exam.
During the semester, students can earn up to 50 points from five-minute tests and the project design (graded together out of 65 points, so up to 15 points can be lost without reducing the semester maximum). To qualify for the exam, a minimum of 35 semester points is required.
The exam is worth another 50 points: 30 points from the final written test and 20 points from the presentation of project results.
Náhradní absolvování
In case of a stay abroad, semester requirements may be fulfilled in an alternative way. The timing of the gap and alternative deadlines must be arranged with the teacher in advance of the leave.
Language of instruction
English
Further Comments
Study Materials
The course is taught annually.
Teacher's information
http://www.youtube.com/watch?v=suQSmEToTdo
The course is also listed under the following terms Autumn 2022, Autumn 2023, Autumn 2024.
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