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.

Language of instruction

Czech

Number of ECTS credits

5

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

There are no prerequisites

Co-requisites

Not applicable.

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.

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.

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

Mid-term exam, project, computer lab assignments.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Not applicable.

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme IT-MSC-2 Master's

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

Type of course unit

 

Lecture

26 hod., optionally

Teacher / Lecturer

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., optionally

Teacher / Lecturer

doc. Ing. Tomáš Martínek, Ph.D.

Syllabus

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

Project

14 hod., optionally

Teacher / Lecturer

doc. Ing. Tomáš Martínek, Ph.D.