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.
Supervisor
Department
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.
Recommended optional programme components
Not applicable.
Recommended or required reading
- Jacques Cohen: Bioinformatics - An introduction for Computer Scientists, ACM Computing Surveys, 2004, Vol. 36, No. 2, p. 122-158.
- Jean-Michel Claverie, Cedric Notredame: Bioinformatics for Dummies, ISBN: 0-7645-1696-5, Wiley Publishing, Inc., 2003.
- Yi-Ping Phoebe Chen: Bioinformatics Technologies, ISBN: 3540208739, Springer, 2005.
- Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter: Základy buněčné biologie, ISBN: 80-902906-0-4, Espero Publishing, 1998.
- Dan K. Krane, Michael L. Raymer: Fundamental Concepts of Bioinformatics, ISBN: 0-8053-4633-3, Benjamin Cummings 2003.
- Fatima Cvrčková: Úvod do praktické bioinformatiky, ISBN: 80-200-1360-1, Academia, 2006.
- Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, ISBN: 0262101068, MIT Press, 2004.
- Andreas D. Baxevanis, B. F. Francis Ouellette: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, ISBN: 0-471-47878-4, Wiley-Interscience, 2005.
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.
Language of instruction
Czech
Work placements
Not applicable.
Course curriculum
- Syllabus of lectures:
- Introduction to bioinformatics
- Basis of molecular biology
- Tools of molecular biology
- Biological databases
- Sequence alignment, dynamic programing, BLAST, FASTA
- Evolutionary models
- Construction of phylogenetic trees
- DNA assembling
- Genomics and gene searching
- Proteins and their prediction
- Computation of RNA secondary structure
- Proteomics, regulatory networks
- Polymorphism of genes
- Biological databases
- Sequence alignment
- Phylogenetic trees
- Protein structure analysis
Syllabus of computer exercises:
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.
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.
Classification of course in study plans
- Programme IT-MGR-2 Master's
branch MPV , any year of study, summer semester, 5 credits, elective
branch MGM , any year of study, summer semester, 5 credits, elective
branch MSK , any year of study, summer semester, 5 credits, elective
branch MIS , any year of study, summer semester, 5 credits, elective
branch MBS , any year of study, summer semester, 5 credits, elective
branch MIN , any year of study, summer semester, 5 credits, elective
branch MMM , any year of study, summer semester, 5 credits, elective
branch MBI , 1. year of study, summer semester, 5 credits, compulsory
Type of course unit
Lecture
26 hours, optionally
Teacher / Lecturer
Syllabus
- Introduction to bioinformatics
- Basis of molecular biology
- Tools of molecular biology
- Biological databases
- Sequence alignment, dynamic programing, BLAST, FASTA
- Evolutionary models
- Construction of phylogenetic trees
- DNA assembling
- Genomics and gene searching
- Proteins and their prediction
- Computation of RNA secondary structure
- Proteomics, regulatory networks
- Polymorphism of genes
Exercise in computer lab
12 hours, optionally
Teacher / Lecturer
Syllabus
- Biological databases
- Sequence alignment
- Phylogenetic trees
- Protein structure analysis