Bioinformatics Tools and Databases   (HF2BAB)

Academic year:

2026/2027.

Attendance requirements:

There are no requirements.

ECTS:

6

Study level:

Study program:

Teachers:

Marija Đ. Gavrović Jankulović, Ph.D.
full professor, Faculty of Chemistry, Studentski trg 12-16, Beograd

Radivoje M. Prodanović, Ph.D.
full professor, Faculty of Chemistry, Studentski trg 12-16, Beograd

Assistant:

Milena O. Zlatanova, Ph.D.
research associate, Faculty of Chemistry, Studentski trg 12-16, Beograd

Hours of instruction:

Weekly: two hours of lectures + two hours of exercises + one hour of study research work

Goals:

To familiarize students with applying bioinformatics tools and methods for gene and genome sequence analysis, analysis of primary, secondary and modeling of the 3D structure of proteins. To train students to use computer programs and internet services in solving problems in biochemistry, molecular biology, and biotechnology.

Outcome:

The student can apply bioinformatics tools and methods for gene and genome sequence analysis, analysis of primary, secondary, and modeling of the 3D structure of proteins, as well as to use them in solving problems in biochemistry, molecular biology, and biotechnology.

Teaching methods:

Lectures, theoretical exercises, seminars.

Extracurricular activities:

—

Coursebooks:

Main coursebooks:

• Andreas D. Baxevanis, Gary D. Bader, David S. Wishart: Bioinformatics - A Practical Guide to the Analysis of Genes and Proteins, John Wiley and Sons, 2020.

Supplementary coursebooks:

• Current Protocols in Bioinformatics, John Wiley and Sons, 2007.
• Arthur M. Lesk: Introduction to Bioinformatics, Oxford University Press, 2002.
• Jonathan Pevsner: Bioinformatics and Functional Genomics, John Wiley and Sons, 2003.
• Thomas Dandekar & Meik Kunz: Bioinformatics, Springer 2023. ISBN 978-3-662-65036-3
• M. Gavrović-Jankulović: Vodič kroz bioinformatičke baze podataka, WUS °ăáâŕŘřĐ MSDP 003/2009
• R. Prodanović: Proteinski inženjering, Univerzitet u Beogradu - Hemijski fakultet, 2019.

Additional material:

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Lectures:

0 points (2 hours a week)

Syllabus:

• Bioinformatics and the Internet.
• NCBI data model.
• Database of gene and genome sequences.
• Database of protein structures.
• Database of gene maps in the genome, protein-coding sequences ENSEMBL.
• Extraction of information from databases using the ENTREZ system.
• Database search and sequence comparison.
• Creation and analysis of multiple sequence comparisons.
• Prediction of gene structure based on DNA sequence.
• Structure prediction using RNA sequences.
• Prediction of secondary and 3D structures of proteins based on amino acid sequence.
• Use of cDNA sequences (EST) to detect protein-coding DNA sequences.
• Modeling of KEGG metabolic pathways.
• Map of the human genome.
• Comparative genome analysis and phylogenetic analysis.
• Atlas of human proteins.
• Bioinformatic methods of analyzing the connection between protein sequence and function in protein engineering and molecular biology (Prosar, Consesus, and Schema and Information Spectroscopy Method for the analysis of protein and nucleotide sequences, etc.)

The literature study will be conducted according to the Journal Club model, or rather a discussion forum, where students, together with teachers, analyze current scientific publications relevant to the topic.

Exercises:

10 points (2 hours a week)

Syllabus:

• Searching for information on the Internet.
• NCBI data model - examples (GenBank, DDBJ, EMBL).
• Searching gene sequences - examples.
• Searching protein sequences - examples.
• Practical use of Internet resources for genome mapping - examples.
• Asking questions to the ENTREZ system - examples.
• Use of the FASTA program to compare protein sequences.
• Use of BLAST programs for sequence comparison (Nt BLAST, Pr BLAST, BLASTh, BLASTn).
• Use of CLUSTAL V and PSI-BLAST programs to predict protein function based on multiple alignment of protein sequences.
• Use of auxiliary programs (ALSKRIPT, AMAS, Jal View) during multiple protein sequence alignment.
• Finding protein-coding DNA sequences using GENESKAN and MZEF programs.
• Prediction of physicochemical properties of proteins using the ExPASy system (pI values, molecular mass, peptide maps, hydrophobicity, transmembrane regions, signaling sequences, potential glycosylation sites).
• Prediction of protein secondary structure using programs PREDATOR, SOPMA, PSIPRED and COILS.
• 3D protein structure prediction (AlfaFold, SWISS-MODEL).
• Phylogenetic analysis using the PHILIP software package and the PhiloBLAST internet service.
• Analysis of metabolic pathways (flux balance analysis).
• The use of computer programs (Vector NTI, SnapGene) in the design of PCR primers, restriction DNA analysis and cloning.
• ProSAR, Schema and consensus protein design using open source bioinformatics programs.

Semester papers:

20 points

Written exam:

60 points

Practical exam:

10 points

Study research work:

0 points (1 hour a week)