Course detail

Bioinformatics

FEKT-ABINAcad. year: 2016/2017

The course is oriented to principles of bioinformatic processing of biological sequences. It is focused on getting knowledge about biological databases, their structure, and possibilities of their use. It is focused on the study of information methods used for analysis of sequences from biological databases including DAN and on the study of terms genomics and proteomics. Students will get experimental knowledge using Matlab that will be used for design of algorithms for acquisition and processing of biological sequences.

Language of instruction

Czech

Number of ECTS credits

5

Mode of study

Not applicable.

Guarantor

prof. Ing. Valentine Provazník, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Offered to foreign students

Of all faculties

Learning outcomes of the course unit

The student will be able to:
- acquire information from biological databasis,
- explain fundamental terms of bioinformatics,
- describe principle of basic methods for analysis of sequences from biological databases,
- discus advantages and disadvantages of the methods,
- design custom methods for sequence analysis based on defined requirements.

Prerequisites

The student should be able to explain fundamental principles of genetics, should know basic terms and laws of molecular biology and should be oriented in basic knowledge of digital signal processing. Generally, knowledge on the level of secondary education is required.

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Techning methods include lectures and computer laboratories. Course is taking advantage of e-learning (Moodle) system. Students have to write projects/assignments during the course.

Assesment methods and criteria linked to learning outcomes

up to 40 points from computer exercises (2 tests and 1 practical work)
up to 60 points from finel written exam
The exam is oriented to verification of orientation in basic terms of bioinformatics, ability to design methods for sequence analysis, apply operations on sequences.

Course curriculum

1. Genome and expression.
2. Genetic code and codon bias.
3. DNA sequencing and databases.
4. Substitution matrices.
5. Basics of dynamical programming.
6. Sequence alignment - global alignment.
7. Sequence alignment - local alignment.
8. Homolog searching.
9. Phylogenetics.
10. Numerical representations of genomic data.
11. Prediction of protein structurs.

Work placements

Not applicable.

Aims

The aim of the course is to inform students about bioinformatics, namely about information structure in biological databases and way of their use and about methods of analysis of sequences acquired from biological databases.

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

Computer exercises are obligatory. Excused absence can be substituted.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

A. D. Baxevanis, B. F. F. Ouellette: Bioinformatics – A Practical Guide to the Analysis of Genes and Proteins. Wiley-Interscience, 2005. ISBN 0-471-47878-4 (EN)
F. Cvrčková: Úvod do praktické bioinformatiky. Praha : Academia, 2006. ISBN 80-200-1360 (CS)
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme BTBIO-A Bachelor's

    branch A-BTB , 2 year of study, summer semester, compulsory

  • Programme EEKR-CZV lifelong learning

    branch EE-FLE , 1 year of study, summer semester, compulsory

Type of course unit

 

Lecture

26 hod., optionally

Teacher / Lecturer

Ing. Denisa Maděránková, Ph.D.

Syllabus

Biological databases: databases of sequences, database mapping, data mining from biological databases, genomic databases. Analysis of nucleotides: prediktivní metody v a. DNA sekvencí, prediktivní metody v a. RNA sekvencí, sekvenční polymorfismus. Analýza na úrovni proteinů: prediktivní metody v a. proteinových sekvencí, predikce struktury proteinů. Metody: porovnávání párů v sekvencích metodou BLAST a FASTA, vytváření a analýza násobných zarovnání sekvencí, metody sestavení zarovnání a jejich zakončení, fylogenetická analýza, výpočetní přístup ke komparativní genomice, proteomika a identifikace proteinů, exprese genů v DNA mikročipech. Využití jazyka MATLAB a Perl pro analýzy biologických dat.

Exercise in computer lab

26 hod., compulsory

Teacher / Lecturer

Ing. Radovan Smíšek, Ph.D.
Ing. Kristýna Kupková
Ing. Denisa Maděránková, Ph.D.

Syllabus

1. Úvod do molekulární biologie, opakování základů Matlab
2. Základní statistika genomických dat
3. Základní statistika genomických dat
4. Databáze a formáty dat
5. Skórovací a substituční matice
6. Globální zarovnávání sekvencí
7. Lokální zarovnávání sekvencí
8. Vícenásobné zarovnávání sekvencí, BLAST
9. Numerické reprezentace
10. Predikce proteinových struktur
11. Konstrukce fylogenetických stromů
12. Numerické reprezentace
13. Speciální témata bioinformatiky