Jan 24, 2020   8:50 a.m. Timotej
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Course syllabus N426A0_4I - Applied Genomics, Proteomics and Bioinformatics (FCFT - WS 2020/2021)

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University: Slovak University of Technology in Bratislava
Faculty: Faculty of Chemical and Food Technology
Course unit code: N426A0_4I
Course unit title: Applied Genomics, Proteomics and Bioinformatics
Mode of completion and Number of ECTS credits: Exam (3 credits)
Course contents:
1.Genomics and its applications. (allowance 14/4)
a.Genomics classification. Introdoction into genomics.
b. Genome sequencing: whole shotgun genome sequencing. Sequencing technology: Sanger capillary sequencing, Roche 454 (pyrosequencing), Illumina/Solexa, SOLiD System. Pros and cons of sequencing techniques.
b.ORF and promoter predictions. Intron and exon splicing predictions. Gene annotation. Major genome databases. Structure, organization and composition of prokaryotic genomes. Transcriptional regulators of bacterial genes. Transposable genetic elements in bacterial genomes. Evolution of bacterial operons and operonisation. Islands and segments of pathogenicity and resistance. Bacterial genome atlas BacMap. Microbial genomics and genomic epidemiology. Metagenomics and methods in metagenomics.
c.Evolution and structure of mitochondrial genomes. Comparative mitochondrial genomics and mitochondrial diseases.Structure and organization of eukaryotic genomes (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, filamentous fungi, Drosophila melanogaster, Caenorhabditis elegans, Homo sapiens). Repetitive and transposable genetic elements and their effect on genome. Telomeric and subtelomeric regions in chromosomes. CpG methylation, RNAi and gene silencing. Yeast two hybrid system. cDNA microarrays.
d.History of human genome sequencing. Human genome evolution and structural variations (STR, VNTR, SNP). Genomics of human diseases. Nutritional genomics. Epigenomics and its methods. Functional genomics and methods: yeast two hybrid system, cDNA microarrays, SAGE, loss of gene function, gain of gene function.

2.Proteomics and its applications. (allowance 6/0)
a.Proteomics classification. Introduction into proteomics.1D SDS PAGE a 2D SDS PAGE. Detection and quantitation of proteins in gels. Pros and cons of various staining methods. Basics of mass spectrometry. Malditof and ESI, and their application in proteomics.
b.Tandem MS/MS spectrometry. Peptide sequencing by tandem mass spectrometry. Affinity purification of protein. TAP tag.
c.Proteomic databases (Pride) and computer programms for predictions of protein domains, modifications, localisations and structure.

3.Bioinformatics (allowance 4/8)
a.Bioinformatics and its application. Major online databases. Practical use of databases. DNA, RNA, proteins in bioinformatics. Amino acid classification. Similarity, homology, local and global sequence alignment. Scoring matrices (PAM, BLOSUM).
b.Pairwise alignment. Dot sequence alignment. BLAST. Types of BLAST. How to use BLAST, FASTA and multiple alignments (Clustal Omega, Clustal W, Muscle, T-coffee).
c.3D structure -- Protein Data Bank in Europe, ArchSchema, DaliLite. RNA a and protein structure prediction. Structural alignments (TM-score, TM-align, NM-align, etc.).

Last modification made by Ing. Tomáš Molnár on 05/20/2019.

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