Bioinformatics

• 26 hrs lectures
• 12 hrs pc labs
• 14 hrs projects

• 58 pts final exam (written part)
• 16 pts mid-term test (written part)
• 12 pts labs
• 14 pts projects

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.
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.

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.

• 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.

1. Introduction to bioinformatics
2. Basis of molecular biology
3. Tools of molecular biology
4. Biological databases
5. Sequence alignment, dynamic programing, BLAST, FASTA
6. Evolutionary models
7. Construction of phylogenetic trees
8. DNA assembling
9. Genomics and gene searching
10. Proteins and their prediction
11. Computation of RNA secondary structure
12. Proteomics, regulatory networks
13. System biology

1. Biological databases
2. Analysis of genome sequences
3. Sequence alignment
4. Phylogenetic trees
5. Gene prediction
6. Protein structure analysis

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: 

1. presence in another laboratory group dealing with the same task. 
2. showing a summary of results to the tutor at the next lab. 
3. 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.

None.