Course detail
Bioinformatics
FEKT-ABINAcad. year: 2013/2014
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
Number of ECTS credits
Mode of study
Offered to foreign students
Learning outcomes of the course unit
- 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
Co-requisites
Planned learning activities and teaching methods
Assesment methods and criteria linked to learning outcomes
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
2. Biological sequences, genomic and proteomic databasis.
3. Basic principles of alignment of biological sequences.
4. Algorithms for alignment of biological sequences.
5. Scoring and scoring systems.
6. Multiple sequence alignment.
7. Fylogenetics and fylogenetic trees.
8. Constructions of fylogenetic trees.
9. Identification of motifs in sequences.
10. Algorithms and optimization of motif identification.
11. Prediction of protein structurs.
Work placements
Aims
Specification of controlled education, way of implementation and compensation for absences
Recommended optional programme components
Prerequisites and corequisites
Basic literature
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
Classification of course in study plans
Type of course unit
Lecture
Teacher / Lecturer
Syllabus
Exercise in computer lab
Teacher / Lecturer
Syllabus
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