Course detail

Advanced methods in Bioinformatics

FEKT-MPA-PMBAcad. year: 2024/2025

The course is mainly oriented towards acquiring practical skills in the field of bioinformatics processing of large datasets. It mainly focuses on analyzes of bacterial genomes and transcriptomes. For the complexity of such analyses, it also brings a basic understanding of working with the command line, creating your own pipelines and using remote calculations. All this while understanding how these analyzes are applicable to the knowledge inference that can be used in medicine, biotechnology or genome engineering.

Current bioinformatics processes large amounts of data that cannot be processed on personal computers. Therefore, it relies on remote calculations on powerful computational servers. This requires the use of a task scheduler and, in cooperation with basic code scripting, gives almost unlimited possibilities even in the analysis of so-called non-model organisms. Computational analyzes can thus be used with great overlap in many scientific disciplines, especially biotechnology, both medical and industrial.

 

Language of instruction

English

Number of ECTS credits

3

Mode of study

Not applicable.

Guarantor

doc. Mgr. Ing. Karel Sedlář, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Offered to foreign students

Of all faculties

Entry knowledge

A student enrolled in this course should be familiar with the principles of algorithms used in bioinformatics for the analysis of sequence similarity, their assembly into longer sections, or algorithms deriving information from the primary structure of the sequence. They must also understand the basic functionality of organisms at the cellular level based on the central dogma of molecular biology.

 

Rules for evaluation and completion of the course

Not applicable.

Aims

The aim of the course is to provide students with advanced knowledge in the field of sequencing data processing through batch jobs and cloud computing using modern computational tools so they are able to set up their own pipelines for complex genome analysis.

A graduate of the course is able to:

- to work with computing resources using batch jobs while using the scheduler

- to perform quality assessment of both genomic and transcriptomic sequencing data

- to assemble the complete genome and annotate it

- to call variants in mutant or otherwise related genomes

- to perform an in-depth analysis of the transcriptome

 

Study aids

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Ohlebusch E.: Bioinformatics Algorithms. Oldenbusch Verlag, 2013. (CS)
Compeau F., Pevzner P.: Bioinformatics Algorithms. Active Learning Publishers, 2015. (CS)
MacLean, D. R Bioinformatics Cookbook. Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis. Packt Publishing, 2019. ISBN 978-1789950694 (EN)
Moorhouse M, Barry P: Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice. Wiley; 1 edition, 2004. (EN)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme MPC-BTB Master's, 2. year of study, summer semester, compulsory-optional
  • Programme MPA-BTB Master's, 2. year of study, summer semester, compulsory-optional

Type of course unit

 

Exercise in computer lab

26 hours, optionally

Teacher / Lecturer

doc. Mgr. Ing. Karel Sedlář, Ph.D.

Syllabus

1. Introduction, metacentrum, sratoolkit, sequencing data quality assesment

2. Trimming, de novo assembly

3. Reference-based assembly, variant calling

4. Genome annotation

5. RNA-Seq preprocessing, mapping

6. RNA-Seq – count table