C3211 Applied bioinformatics

Faculty of Science
Spring 2023
Extent and Intensity
0/4. 3 credit(s). Type of Completion: k (colloquium).
Teacher(s)
prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer)
Mgr. Josef Houser, Ph.D. (seminar tutor)
Mgr. Lenka Malinovská, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Michaela Wimmerová, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Prerequisites
Basic knowledge of biomacromolecules
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 15 student(s).
Current registration and enrolment status: enrolled: 7/15, only registered: 0/15, only registered with preference (fields directly associated with the programme): 0/15
Course objectives
At the end of the course students should be able to utilize bioinformatic tools for solving biological problems and for optimization of experimental laboratory research.
Learning outcomes
At the end of the course students should: 1) Obtain basic knowledge of bioinformatics. Students should be able to: 1) Process bioinformational data. 2) Predict basic properties of biomacromolecules. 3) Utilize bioinformational tools for solving of biological problems.
Syllabus
  • Basic protein properties: theoretical background (proteinogenic amino acids, non-standard proteinogenic amino acids, isoelectric point, extinction coefficient, stability and storage of proteins, localization in cell), prediction of basic protein properties, initial methionine and its cleavage, signal sequence, information in databases, sequence alignment.
  • Recombinant proteins production: theoretical background (vectors, host organisms, ligation, transformation, expression, problems, disulfide bonds, posttranslational modifications, rare codons, production of toxic proteins), prediction of posttranslational modifications and disulfide bonds, prediction of glycosylation, design of synthetic genes.
  • Secondary structure and function of proteins: theoretical background (secondary structure and protein folding, CD spectroscopy, prediction of protein function, secondary protein databases), secondary structure prediction, CD spectrum prediction, prediction of function by sequence alignment, identification and analysis of active site, mutations in active sites, identification of structural and functional motifs in sequences.
  • Protein tertiary structure and oligomerization: theoretical background (3D structure, structural databases, structure determination, RTG, NMR, theory of structure prediction, importance of oligomerization, determination of oligomerization), 3D structure visualization, types of depiction, homology proteins alignment, active site analysis, prediction tools, model validation, prediction of oligomerization, repetition analysis.
Literature
    recommended literature
  • ŠMARDA, Jan, Jiří DOŠKAŘ, Roman PANTŮČEK, Vladislava RŮŽIČKOVÁ and Jana KOPTÍKOVÁ. Metody molekulární biologie (Methods of molecular biology). 2. dotisk 1. vydání. Brno: Masarykova univerzita, 2010. 194 pp. ISBN 978-80-210-3841-7. info
  • XIONG, Jin. Essential bioinformatics. 1st pub. Cambridge: Cambridge University Press, 2006. xi, 339. ISBN 0521600820. info
Teaching methods
Lectures, practical exercises in silico, educational excursions.
Assessment methods
Final test, oral exam.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught: every other week.
Teacher's information
The teaching during the semester is irregular, based on agreement with students.
The course is also listed under the following terms Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/spring2023/C3211