Course: Bioinformatics for Biologists

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Course title Bioinformatics for Biologists
Course code KMB/613
Organizational form of instruction Lecture + Lesson
Level of course Doctoral
Year of study not specified
Frequency of the course In academic years starting with an even year (e.g. 2016/2017), in the summer semester.
Semester Summer
Number of ECTS credits 6
Language of instruction English
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Novák Petr, Ing. Ph.D.
Course content
Content of lectures: 1. What is bioinformatics, typical bioinformatics problems, types of biological data, introduction to databases 2. Databases, database structure, most important databases of biological information and online services, NCBI, EMBL-EBI, ELIXIR infrastructure 3. DNA and protein sequences, sequence alignment, pairwise and multiple alignment 4. Position specific substitution matrices, profiles, hidden Markov models, PSI-BLAST 5. NCBI blast, searching sequence databases 6. DNA sequencing, assembly, genome assembly, contig, scaffold, next generation sequencing 7. Genome architecture and evolution, genome annotation, gene prediction, comparative genomics 8. Gene expression analysis, microarrays, RNA-Seq, ChiP-Seq, EST 9. Gene ontologies, signal pathways 10. Molecular phylogenetics 11. "omics" data, high throughput technologies, processing of "big data", algorithms for clustering 12. Structural bioinformatics: protein structure analysis - protein surface, charge, conserved residue, motifs, protein function prediction 13. Structural bioinformatics: prediction of 3D structure, ab initio prediction, homology modelling, protein structure databases 14. Molecular interaction, docking, virtual screening, drug design and discovery Content of practicals: Student will learn how to uses methods introduced in lectures

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Demonstration, Laboratory, E-learning
  • Class attendance - 40 hours per semester
  • Preparation for exam - 50 hours per semester
Learning outcomes
The aim of this course is to introduce students with specialization in biology to the new field of bioinformatics. Students will learn about basic algorithms and tools for analysis of data in biology, how to use databases and bioinformatics software.

Prerequisites
Understanding of molecular biology and genetics KMB/023 KMB/250

Assessment methods and criteria
Oral examination, Analysis of student's work activities (technical works), Test

Recommended literature
  • Fatima Cvrčková: Úvod do praktické bioinformatiky, Academia, Praha, 2006.
  • Jin Xiong: Essential Bioinformatics, Cambridge University Press, 2006.
  • Marketa J. Zvelebil, Jeremy O. Baum: Understanding Bioinformatics, Garland Science, 2008.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Infection Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Physiology and Developmental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Infection Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Infection Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Physiology and Developmental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Fyziologie a vývojová biologie (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Physiology and Developmental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: -
Faculty: Faculty of Science Study plan (Version): Experimental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer