Course detail

Bioinformatics

FIT-BIFAcad. year: 2021/2022

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.

Language of instruction

Czech

Number of ECTS credits

Mode of study

Not applicable.

Guarantor

doc. 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

Not applicable.

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Not applicable.

Assesment methods and criteria linked to learning outcomes

Mid-term exam, project, computer lab assignments.

Course curriculum

Not applicable.

Work placements

Not applicable.

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

Presence in any form of instruction is not compulsory. An absence (and hence loss of points) can be compensated in the following ways: 
  1. presence in another laboratory group dealing with the same task. 
  2. showing a summary of results to the tutor at the next lab. 
  3. sending a short report (summarizing the results of the missed lab and answering the questions from the assignment) to the tutor, in 14 days after the missed lab.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

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.
Dan K. Krane, Michael L. Raymer: Fundamental Concepts of Bioinformatics, ISBN: 0-8053-4633-3, Benjamin Cummings 2003.
Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, ISBN: 0262101068, MIT Press, 2004.
Supratim Choudhuri: Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools, ISBN: 978-0124104716, Academic Press, 2014

Recommended reading

Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter: Základy buněčné biologie, ISBN: 80-902906-0-4, Espero Publishing, 1998.
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.
Dan K. Krane, Michael L. Raymer: Fundamental Concepts of Bioinformatics, ISBN: 0-8053-4633-3, Benjamin Cummings 2003.
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.
Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, ISBN: 0262101068, MIT Press, 2004.
Supratim Choudhuri: Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools, ISBN: 978-0124104716, Academic Press, 2014
Yi-Ping Phoebe Chen: Bioinformatics Technologies, ISBN: 3540208739, Springer, 2005.

Classification of course in study plans

  • Programme IT-MSC-2 Master's

    branch MBI , 1 year of study, summer semester, compulsory
    branch MBS , 0 year of study, summer semester, elective
    branch MGM , 0 year of study, summer semester, elective
    branch MIN , 0 year of study, summer semester, elective
    branch MIS , 0 year of study, summer semester, elective
    branch MMM , 0 year of study, summer semester, elective
    branch MPV , 0 year of study, summer semester, elective
    branch MSK , 0 year of study, summer semester, elective

  • Programme MITAI Master's

    specialization NADE , 0 year of study, summer semester, elective
    specialization NBIO , 1 year of study, summer semester, compulsory
    specialization NCPS , 0 year of study, summer semester, elective
    specialization NEMB , 0 year of study, summer semester, elective
    specialization NGRI , 0 year of study, summer semester, elective
    specialization NHPC , 0 year of study, summer semester, elective
    specialization NIDE , 0 year of study, summer semester, elective
    specialization NISD , 0 year of study, summer semester, elective
    specialization NMAL , 0 year of study, summer semester, elective
    specialization NMAT , 0 year of study, summer semester, elective
    specialization NNET , 0 year of study, summer semester, elective
    specialization NSEC , 0 year of study, summer semester, elective
    specialization NSEN , 0 year of study, summer semester, elective
    specialization NSPE , 0 year of study, summer semester, elective
    specialization NVER , 0 year of study, summer semester, elective
    specialization NVIZ , 0 year of study, summer semester, elective
    specialization NISY up to 2020/21 , 0 year of study, summer semester, elective
    specialization NISY , 0 year of study, summer semester, elective

Type of course unit

 

Lecture

26 hod., optionally

Teacher / Lecturer

Ing. Miloš Musil, Ph.D.
Ing. Ivana Burgetová, Ph.D.
doc. 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 hod., compulsory

Teacher / Lecturer

Ing. Miloš Musil, Ph.D.

Syllabus

  1. Biological databases
  2. Analysis of genome sequences
  3. Sequence alignment
  4. Phylogenetic trees
  5. Gene prediction
  6. Protein structure analysis

Project

14 hod., compulsory

Teacher / Lecturer

Ing. Miloš Musil, Ph.D.

Syllabus

A project will be assigned to each student. Implementation, presentation and documentation of the project will be evaluated.