FEKT-ABINAcad. year: 2017/2018
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.
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.
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.
Recommended optional programme components
Recommended or required reading
F. Cvrčková: Úvod do praktické bioinformatiky. Praha : Academia, 2006. ISBN 80-200-1360 (CS)
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)
Rosypal, S. Nový přehled biologie. Scientia, Praha 2003. ISBN 80-7183-268-5 (CS)
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.
Language of instruction
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.
10. Numerical representations of genomic data.
11. Prediction of protein structurs.
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.