PřF:E7492 DNA Sequence Analysis - Course Information
E7492 DNA Sequence Analysis
Faculty of ScienceAutumn 2024
- Extent and Intensity
- 2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
- 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 - Prerequisites
- Students need to understand basic principles of molecular biology and genetics.
- 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: 0/30, only registered: 16/30, only registered with preference (fields directly associated with the programme): 0/30 - Course objectives
- The goal of the course is to teach the student to assemble DNA sequences, to understand the structure and use of genetic databases, to evaluate a DNA sequence and to identify it with respect to the biodiversity context using phylogenetic analyses.
- Learning outcomes
- After completing the course the student will be able:
- to formulate a hypothesis and to test it;
- to use information available in genetic databases;
- to identify an unknown sequence by searching the genetic databases and comparing the hits with suitable BLAST algorithms;
- to evaluate the sequence identification;
- to calculate genetic distances, using suitable substitution model;
- to reconstruct phylogenetic trees, using distance methods, maximum parsimony, maximum likelihood and Bayesian inference;
- to interpret phylogenetic relationships in a sequence dataset and critically evaluate conflicting results. - Syllabus
- 1. Genomics: (a) Genomes, genome organisation, variability, (b) Genome sequencing – next-gen sequencing, pyrosequencing, sequencing by ligation.
- 2. Genome assembly: (a) De-novo, resequencing, mutation detection, (b) Contig, length and number of contigs, (c) Parameters of contig assembly, (d) Coverage – variability detection.
- 3. Sequence search: (a) GenBank, EMBL, DDBJ, UniProt, (b) Entréz, SRS, (c) Libraries, cross-referencing.
- 4. BLAST: (a) nucleotide and protein blast, megablast, psi-blast, (b) Search principle, (c) Result evaluation, E-value.
- 5. Genomic sequence annotation: (a) RNA prediction, (b) Genomic islands, (c) Protein prediction – Prokaryota.
- 6. Genomic sequence annotation: (a) Protein prediction – Eukaryota, (b) CpG islands, (c) Annotation report.
- 7. Alignment: (a) Homologous positions, (b) Local, global alignment – assembly options, (c) Dynamic programming.
- 8. Relationship modelling: (a) Phylogenetic tree - terminology, interpretation, (b) Tree comparison.
- 9. Substitution model: (a) Genetic distances, (b) Model parameters, (c) Problems and solutions.
- 10. Phylogenetics: (a) Phylogenetic analysis – neighbour-joining, maximum parsimony, (b) Significance of signal, bootstrap.
- 11. Maximum likelihood: (a) Likelihood function, (b) Randomised accelerated maximum likelihood.
- 12. Bayesian analysis: (a) Posterior probability, (b) Effect of priors on posterior distribution, (c) Convergence, Metropolis-coupled MCMC.
- 13. Gene and species evolution: (a) Supermatrix, (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, discussion, in-class data analysis.
- Assessment methods
- Five-minute tests throughout the course, final project based on student's design, verbal interpretation of the project for the final exam, final written test.
- Language of instruction
- English
- Further Comments
- The course is taught annually.
The course is taught: every week. - Teacher's information
- http://www.youtube.com/watch?v=suQSmEToTdo
- Enrolment Statistics (recent)
- Permalink: https://is.muni.cz/course/sci/autumn2024/E7492