C2138 Advanced bioinformatics

Faculty of Science
Spring 2023
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer)
Mgr. Josef Houser, Ph.D. (lecturer)
Mgr. Lenka Malinovská, Ph.D. (lecturer)
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
Tue 13:00–14:50 C04/118
Prerequisites
C2135 Bioinformatics for practice && NOW ( C2139 Advanced bioinformatics - seminary )
C2130 Introduction to chemoinformatics and bioinformatics C2135
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of this course is to teach students how 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;
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) Summary of basic bioinformatical methods and tools for protein studies.
    2) Summary of basic bioinformatical methods and tools for amino acid and saccharide studies.
    3) Gene expression studies by bioinformatics. Promotor prediction, non-coding regions, transcription factors.
    4) Analysis of sequencing outputs.
    5) Genome annotation. Automatic annotation, its correctness, sources of mistakes. 6) Phylogenetic analysis, phylogenetic trees, principals.
    7) Posttranslational modifications and their importance. Prediction algorithms.
    8) Bioinformatical potential of saccharides, glycome.
    9) Protein data bank (PDB) , 3D structure validation, origin of mistakes in structural data.
    10) Prediction tools for nucleic acids. 2D and 3D structure, repetitions, importance.
    11) Metabolic pathways alignment, metabolome.
    12) Virtual screening in bioinformatics, specificities of databases, protein binding sites.
Literature
  • HODGMAN, T. Charlie, Andrew FRENCH and David R. WESTHEAD. Bioinformatics. 2nd ed. New York: Taylor & Francis, 2010. x, 340. ISBN 9780415394949. URL info
  • ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008. xxiii, 772. ISBN 9780815340249. info
  • MOUNT, David W. Bioinformatics : sequence and genome analysis. 2nd ed. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004. xii, 692. ISBN 0879697121. info
Teaching methods
lectures with practical demonstrations
Assessment methods
written exam
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022.
  • Enrolment Statistics (recent)
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