PřF:Bi7492 DNA Sequence Analysis - Course Information

Bi7492 DNA Sequence Analysis

Extent and Intensity

2/1. 3 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

doc. Mgr. Natália Martínková, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Ladislav Dušek, Ph.D.
RECETOX – Faculty of Science
Supplier department: RECETOX – Faculty of Science

Timetable

Tue 9:00–11:50 F01B1/709

Prerequisites

Students need to understand basic principles of molecular biology and genetics. Suggested courses are Neparametrické metody (K. Kubošová) and Stochastické modely (M. Budíková).

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: 0/30, only registered with preference (fields directly associated with the programme): 0/30

Course objectives

After completing the course the student will be able:
- to formulate a hypothesis and to test it;
- to assemble a complete DNA sequence, using graphical output from sequencing;
- 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

Czech

Further Comments

Study Materials

Teacher's information

http://www.youtube.com/watch?v=suQSmEToTdo

• Enrolment Statistics (Autumn 2013, recent)
  
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