Course detail

Bioinformatics

FIT-BIFAcad. year: 2017/2018

This course introduces students to basic principles of molecular biology, present algorithms pro biological data analysis, describes their time complexity and shows direction how to design the new methods very effectively. Particularly, the following algorithms will be discussed: methods for sequence alignment, evolutionary models, construction of phylogenetic trees, algorithms for gene identification using machine learning and approaches for prediction of 2D and 3D protein structure. Lectures will be supplement with practical examples using available biological databases.

Supervisor

Ing. Tomáš Martínek, Ph.D.

Department

Department of Computer Systems (UPSY)

Learning outcomes of the course unit

Students will be able to take advantages of large biological database and design new efficient algorithms for their analysis.

Understanding the relations between computers (computing) and selected molecular processes.

Prerequisites

There are no prerequisites

Co-requisites

Not applicable.

Recommended optional programme components

Not applicable.

Recommended or required reading

  • Jacques Cohen: Bioinformatics - An introduction for Computer Scientists, ACM Computing Surveys, 2004, Vol. 36, No. 2, p. 122-158.
  • Jean-Michel Claverie, Cedric Notredame: Bioinformatics for Dummies, ISBN: 0-7645-1696-5, Wiley Publishing, Inc., 2003.
  • Yi-Ping Phoebe Chen: Bioinformatics Technologies, ISBN: 3540208739, Springer, 2005.
  • Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter: Základy buněčné biologie, ISBN: 80-902906-0-4, Espero Publishing, 1998.

  • Dan K. Krane, Michael L. Raymer: Fundamental Concepts of Bioinformatics, ISBN: 0-8053-4633-3, Benjamin Cummings 2003.
  • Fatima Cvrčková: Úvod do praktické bioinformatiky, ISBN: 80-200-1360-1, Academia, 2006.
  • Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, ISBN: 0262101068, MIT Press, 2004.
  • Andreas D. Baxevanis, B. F. Francis Ouellette: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, ISBN: 0-471-47878-4, Wiley-Interscience, 2005.


Planned learning activities and teaching methods

Not applicable.

Assesment methods and criteria linked to learning outcomes

Study evaluation is based on marks obtained for specified items. Minimimum number of marks to pass is 50.

None.

Language of instruction

Czech

Work placements

Not applicable.

Course curriculum

    Syllabus of lectures:
    1. Introduction to bioinformatics
    2. Basis of molecular biology
    3. Tools of molecular biology
    4. Biological databases
    5. Sequence alignment, dynamic programing, BLAST, FASTA
    6. Evolutionary models
    7. Construction of phylogenetic trees
    8. DNA assembling
    9. Genomics and gene searching
    10. Proteins and their prediction
    11. Computation of RNA secondary structure
    12. Proteomics, regulatory networks
    13. Polymorphism of genes

    Syllabus of computer exercises:
    1. Biological databases
    2. Sequence alignment
    3. Phylogenetic trees
    4. Protein structure analysis

    Syllabus - others, projects and individual work of students:
    A project will be assigned to each student. Implementation, presentation and documentation of the project will be evaluated.

Aims

To understand the principles of molecular biology. To perceive the basic used algorithms and to well informed about relevant biological databases. To be able to design new effective methods for biological data analysis.

Specification of controlled education, way of implementation and compensation for absences

Mid-term exam, project, computer lab assignments.

Classification of course in study plans

  • Programme IT-MGR-2 Master's

    branch MPV , any year of study, summer semester, 5 credits, elective
    branch MGM , any year of study, summer semester, 5 credits, elective
    branch MSK , any year of study, summer semester, 5 credits, elective
    branch MIS , any year of study, summer semester, 5 credits, elective
    branch MBS , any year of study, summer semester, 5 credits, elective
    branch MIN , any year of study, summer semester, 5 credits, elective
    branch MMM , any year of study, summer semester, 5 credits, elective
    branch MBI , 1. year of study, summer semester, 5 credits, compulsory

Type of course unit

 

Lecture

26 hours, optionally

Teacher / Lecturer

Ing. Tomáš Martínek, Ph.D.

Syllabus


  1. Introduction to bioinformatics
  2. Basis of molecular biology
  3. Tools of molecular biology
  4. Biological databases
  5. Sequence alignment, dynamic programing, BLAST, FASTA
  6. Evolutionary models
  7. Construction of phylogenetic trees
  8. DNA assembling
  9. Genomics and gene searching
  10. Proteins and their prediction
  11. Computation of RNA secondary structure
  12. Proteomics, regulatory networks
  13. Polymorphism of genes

Exercise in computer lab

12 hours, optionally

Teacher / Lecturer

Ing. Tomáš Martínek, Ph.D.

Syllabus


  1. Biological databases
  2. Sequence alignment
  3. Phylogenetic trees
  4. Protein structure analysis

Project

14 hours, optionally

Teacher / Lecturer

Ing. Tomáš Martínek, Ph.D.