Course detail
Bioinformatics
FIT-IV108Acad. year: 2022/2023
An advanced course in bioinformatics (lecture and computer lab) building upon elementary mol.biology and/or bioinformatics courses.
State doctoral exam - topics:
- Searching in biological sequences (types of searches, principles, and applications)
- Comparison of biological sequences (pairwise and multiple sequence alignment and their applications)
- Genomes, their structure, and DNA sequence analysis
- Analysis and prediction of RNA structure
- DNA sequencing technologies (principles and applications)
- Structure and function of proteins
- Protein sequence analysis (domain detection, structure prediction, analysis of correlated mutations)
- Special DNA structures (triplex, quadruplex), repetitive and mobile DNA, the human genome
- Biological and bioinformatics databases (e.g., GenBank, UniProt, RefSeq, PDB, Gene ontology)
- Computational tools (e.g., BLAST, BLAT, RF/Bioconductor, Biomart, genomic browsers) and data formats (e.g., FASTA, FASTQ, SAM, VCF, GFF3, PDB) used in molecular biology and bioinformatics
Language of instruction
Mode of study
Guarantor
Department
Learning outcomes of the course unit
- understand the inner workings of selected algorithms, their advantages and disadvanteges, including knowledge of recent alternatives
- be able to work with 3-D models of molecules
- be able to evaluate or design methods for solving current problems in bioinformatics
- understand the principles of existing DNA sequencing methods and processing sequencing data
Prerequisites
Co-requisites
Planned learning activities and teaching methods
Assesment methods and criteria linked to learning outcomes
Course curriculum
Work placements
Aims
Specification of controlled education, way of implementation and compensation for absences
Recommended optional programme components
Prerequisites and corequisites
Basic literature
Recommended reading
Zvelebil M., Baum J.: Understanding bioinformatics. Garland Science, London, 2007 ISBN 978-0815340249.
Classification of course in study plans
- Programme DIT Doctoral 0 year of study, winter semester, compulsory-optional
- Programme DIT Doctoral 0 year of study, winter semester, compulsory-optional
- Programme DIT-EN Doctoral 0 year of study, winter semester, compulsory-optional
- Programme DIT-EN Doctoral 0 year of study, winter semester, compulsory-optional
- Programme CSE-PHD-4 Doctoral
branch DVI4 , 0 year of study, winter semester, elective
- Programme CSE-PHD-4 Doctoral
branch DVI4 , 0 year of study, winter semester, elective
- Programme CSE-PHD-4 Doctoral
branch DVI4 , 0 year of study, winter semester, elective
- Programme CSE-PHD-4 Doctoral
branch DVI4 , 0 year of study, winter semester, elective
Type of course unit
Lecture
Teacher / Lecturer
Syllabus
- Biological language (sequence segmentation, information-statistical analysis of biological sequences)
- Pattern matching (algorithms based on filtration and suffix arrays)
- Heuristic algorithms for similarity searching in biological sequences (BLAST, BLAT, Pattern Hunter)
- Regular expressions in bioinformatics
- Algorithms for analysis and prediction of structural data (secondary structure, contacts inb proteins, domain identification)
- Algorithms for analysis and prediction of structural data (3D structure, structural comparisons)
- Working with molecular structures in Pymol
- New methods of DNA sequencing
- Genome assembly and other operations on short nucleic acid sequences
- Prediction of melting temperature in DNA and other nucleic acids (program mfold)
- RNA secondary structure
- DNA computing
- Comparative genomics of human (analysis of scientific papers)
Guided consultation in combined form of studies
Teacher / Lecturer