SubjectsSubjects(version: 855)
Course, academic year 2019/2020
  
Databases and computer tools in biochemical research - M320015
Title: Databáze a počítačové nástroje v biochemickém výzkumu
Guaranteed by: Department of Biochemistry and Microbiology (320)
Actual: from 2019
Semester: summer
Points: summer s.:2
E-Credits: summer s.:2
Examination process: summer s.:
Hours per week, examination: summer s.:0/2 MC [hours/week]
Capacity: unknown / unlimited (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Guarantor: Šantrůček Jiří Ing. Ph.D.
Leonhardt Tereza Ing. Ph.D.
Interchangeability : N320040
Examination dates   Schedule   
This subject contains the following additional online materials
Annotation -
Last update: Hladíková Jana (13.12.2017)
The course objectives include: introduction to fundamental bioinformatic approaches and tools allowing analyzing nucleotide and protein sequences, including critical interpretation of analysis outputs; survey of potential uses of bioinformatic analyses to address experimental tasks; and detailed insight into practical aspects of related molecular biology and proteomic methods and approaches.
Aim of the course -
Last update: Hladíková Jana (13.12.2017)

Students will be able to:

Use publicly accessible bioinformatics tools and nucleotide and protein databases.

Independently design a strategy to analyze the sequence data, critically interpret the outcome of analyses and propose an experimental approach to prove the in silico predictions correct.

Taking advantage from bioinformatic analyses of nucleotide and protein sequences, propose complex, feasible solution for a successful molecular biology experiment.

Literature -
Last update: Šantrůček Jiří Ing. Ph.D. (23.01.2018)

R: Cvrčková F., Úvod do praktické bioinformatiky, Academia, 2006, ISBN 80-200-1360-1

A: Twyman R., Principles of Proteomics, Garland Science, 2013, ISBN 978-0815344728

A: Green M.R., Sambrook J., Molecular Cloning: A Laboratory Manual (4th ed.), Cold Spring Harbor Laboratory Press, 2012, ISBN 1936113422

Learning resources -
Last update: Šantrůček Jiří Ing. Ph.D. (23.01.2018)

https://www.ncbi.nlm.nih.gov/

https://www.ebi.ac.uk/services

https://www.expasy.org/

https://www.uniprot.org/

https://omictools.com/

Syllabus -
Last update: Šantrůček Jiří Ing. Ph.D. (23.01.2018)

1. Bioinformatics, cross-database search platforms for data mining.

2. Databases and software for nucleotide sequence analyses.

3. Gene function predictions, prediction of promoters and regulatory elements.

4. Design and practical aspects of PCR experiment.

5. Central dogma upturned: a strategy to isolate coding sequence.

6. Practical aspects and method selection in DNA and DNA-binding protein analyses.

7. Practical aspects and method selection in RNA and transcript level analyses.

8. Proteomic servers and databases. Tools for protein sequence alignments.

9. Protein modifications. In silico prediction and experimental proof.

10. Protein secondary structure and hydropathy profile. In silico prediction and experimental proof.

11. Protein quaternary structure and oligomerization state. In silico prediction and experimental proof.

12. Membrane proteins. Determination of protein topology in biological membrane, the surface properties of proteins and detergents.

13. Native state of protein. Intracellular localization and interactions of protein.

14. Gene ontology. Processing of data from proteomic experiments.

Registration requirements -
Last update: Hladíková Jana (13.12.2017)

Molecular Biology

Genetic Engineering

Course completion requirements -
Last update: Šantrůček Jiří Ing. Ph.D. (23.01.2018)

The course is finished with working out of an individual project and its successful defense.

Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0,2 6
Obhajoba individuálního projektu 0,1 2
Práce na individuálním projektu 0,7 20
Účast na seminářích 1 28
2 / 2 56 / 56
Coursework assessment
Form Significance
Defense of an individual project 100

 
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