Course details

Bioinformatics

BIF Acad. year 2020/2021 Summer semester 5 credits

Current academic year

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.

Guarantor

Martínek Tomáš, doc. Ing., Ph.D. (DCSY)

Course coordinator

Burgetová Ivana, Ing., Ph.D. (DIFS)

Language of instruction

Czech

Completion

Examination (written)

Time span

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

Assessment points

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

Department

Department of Computer Systems (UPSY)

Lecturer

Burgetová Ivana, Ing., Ph.D. (DIFS)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY)

Instructor

Musil Miloš, Ing., Ph.D. (DIFS)

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.
Understanding the relations between computers (computing) and selected molecular processes.

Learning objectives

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.

Syllabus of lectures

  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. Polymorphism of genes

Syllabus of computer exercises

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

Progress assessment

Mid-term exam, project, computer lab assignments.
Exam prerequisites:
None.

Controlled instruction

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.

Exam prerequisites

None.

Course inclusion in study plans

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