PřF:C2139 Advanced bioinformatics - semi - Course Information

C2139 Advanced bioinformatics - seminary

Extent and Intensity

0/1. 1 credit(s) (plus extra credits for completion). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer)
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

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

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. Milton Park, Abingdon: Taylor & Francis, 2010, x, 340. ISBN 9780415394949. 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. New York: Cold Spring Harbor Laboratory Press, 2001, xii, 564 s. ISBN 0-87969-597-8. info

Teaching methods

practical exercises

Assessment methods

written test

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.
The course is taught: every week.

Listed among pre-requisites of other courses

• C2138 Advanced bioinformatics
  C2135 && NOW(C2139)  

• Enrolment Statistics (Spring 2014, recent)
  
• Permalink: https://is.muni.cz/course/sci/spring2014/C2139