C2139 Advanced bioinformatics - seminary

Faculty of Science
Spring 2019
Extent and Intensity
0/1/0. 1 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer), doc. RNDr. Radka Svobodová, Ph.D. (deputy)
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
Timetable
Mon 18. 2. to Fri 17. 5. Tue 16:00–16:50 C04/118
Prerequisites
NOW ( C2138 Advanced bioinformatics )
NOW (C2138 Advanced Bioinformatics)
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
At the end of the course students should be able to:
understand and explain basic terms in the field of bioinformatics;
compare large databases of sequences and extract data;
predict 2D and 3D structure of proteins and nucleic acids;
predict posttranslational modifications;
work with bioinformatic tools
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
  • 1) interface among basic bioinformatic tools (database search, sequence alignment, prediction of genes and proteins, primer design, etc) WorkBench.
    2) Manipulation of sequence outputs - BioEdit.
    3) Study of gene expression using bioinformatics. Promoter prediction, non-coding parts of nucleic acids, binding sites for transcription factors (TRANSFAC).
    4) Study of gene expression using bioinformatics. Prediction of transcription factors (Hidden Markov Models).
    5) Genomes annotation. Automation (GeneQuiz, PEDANT, ERGO), verification, error sources
    6) Genome annotation. Prediction of protein functions using comparison of conserved operons (COGs, STRING).
    7) Phylogenetic analysis, phylogeny trees, software phylogeny trees creation and analysis.
    8) Posttranslational modifications, Prediction of posttranslational modifications (glycosylation).
    9) Bioinformatic potential of saccharides, Saccharide databases, glycome. Structure and biological activity of saccharides (Consortium for Functional Glycomics).
    8) Protein data bank (PDB). Overview, structure information. additional information. Structural data validation.
    9) Prediction tool for nucleic acids. 2D, 3D structure, repetition analysis.
    10) Primer design, mutagenesis. Different approaches in primer design for different purposes. Mutagenesis in vitro and in silico. Site-directed and random mutagenesis.
    11) Alignment of metabolic pathways. Enzyme databases. Combination of enzyme data and their metabolites
    12) Virtual screening in bioinformatics, binding sites of proteins. Molecular docking basics.
Literature
  • HODGMAN, T. Charlie, Andrew FRENCH and David R. WESTHEAD. Bioinformatics. 2nd ed. New York: Taylor & Francis. x, 340. ISBN 9780415394949. 2010. URL info
  • ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science. xxiii, 772. ISBN 9780815340249. 2008. info
  • MOUNT, David W. Bioinformatics : sequence and genome analysis. New York: Cold Spring Harbor Laboratory Press. xii, 564 s. ISBN 0-87969-597-8. 2001. info
Teaching methods
practical exercises
Assessment methods
written test
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024.
  • Enrolment Statistics (Spring 2019, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2019/C2139