BIF Acad. year 2020/2021 Summer semester 5 credits
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.
Language of instruction
Subject specific learning outcomes and competences
Students will be able to take advantages of large biological database and design new efficient algorithms for their analysis.
Generic learning outcomes and competences
Understanding the relations between computers (computing) and selected molecular processes.
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.
Why is the course taught
Biological data analysis requires a knowledge of basic bioinformatics algorithms and tools (sequence alignment, phylogenetic tree construction, assembling/mapping of sequencing data, etc.). The goal of this course is to provide this information for the students and prepare them for a future profession in the area of bioinformatics.
- 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.
- Supratim Choudhuri: Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools, ISBN: 978-0124104716, Academic Press, 2014
- Dan K. Krane, Michael L. Raymer: Fundamental Concepts of Bioinformatics, ISBN: 0-8053-4633-3, Benjamin Cummings 2003.
- 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.
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
Syllabus of computer exercises
- Biological databases
- Analysis of genome sequences
- Sequence alignment
- Phylogenetic trees
- Gene prediction
- Protein structure analysis
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.
Mid-term exam, project, computer lab assignments.
Presence in any form of instruction is not compulsory. An absence (and hence loss of points) can be compensated in the following ways:
- presence in another laboratory group dealing with the same task.
- showing a summary of results to the tutor at the next lab.
- sending a short report (summarizing the results of the missed lab and answering the questions from the assignment) to the tutor, in 14 days after the missed lab.
Course inclusion in study plans
- Programme IT-MSC-2, field MBI, 1st year of study, Compulsory
- Programme IT-MSC-2, field MBS, MGM, MIN, MIS, MMM, MPV, MSK, any year of study, Elective
- Programme MITAI, specialisation NADE, NCPS, NEMB, NGRI, NHPC, NIDE, NISD, NISY, NMAL, NMAT, NNET, NSEC, NSEN, NSPE, NVER, NVIZ, any year of study, Elective
- Programme MITAI, specialisation NBIO, 1st year of study, Compulsory