Course details
Bioinformatics
IV108 Acad. year 2023/2024 Winter semester
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
Guarantor
Language of instruction
Completion
Time span
- 13 hrs lectures
- 13 hrs exercises
Assessment points
- 100 pts final exam
Department
Learning objectives
Introduction to selected algorithms and methods of analysis used in bioinformatics.
At the end of the course, the students will:
- 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
Study literature
- BROWN, Stuart M. Next-generation DNA sequencing informatics. Second edition. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, [2015]. ISBN 978-1621821236.
- Zvelebil M., Baum J.: Understanding bioinformatics. Garland Science, London, 2007 ISBN 978-0815340249.
Syllabus of lectures
- 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)
Progress assessment
Continouous solving exercices, final exam, min 50 points.
Course inclusion in study plans
- Programme DIT, any year of study, Compulsory-Elective group O
- Programme DIT, any year of study, Compulsory-Elective group O
- Programme DIT-EN (in English), any year of study, Compulsory-Elective group O
- Programme DIT-EN (in English), any year of study, Compulsory-Elective group O
- Programme VTI-DR-4, field DVI4, any year of study, Elective
- Programme VTI-DR-4, field DVI4, any year of study, Elective
- Programme VTI-DR-4 (in English), field DVI4, any year of study, Elective
- Programme VTI-DR-4 (in English), field DVI4, any year of study, Elective