Bioinformatics   (451B2)

Academic year:

2023/2024.

Attendance requirements:

There are no requirements.

ECTS:

4

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
associate researcher, Faculty of Chemistry, Studentski trg 12-16, Beograd

Hours of instruction:

Weekly: one hour of lectures + three hours of exercises (1+3+0)

Goals:

To introduce the students with the application of bioinformatics tools and methods for analysis of protein structure and sequence of the gene. Training students to use computer programs and internet services to solve problems in biochemistry and biotechnology.

Outcome:

The student is trained to apply the bioinformatics tools and methods for the analysis of protein structure and sequence of the gene, as well as to use in solving the problems in biochemistry and biotechnology.

Teaching methods:

Lectures, theoretical exercises, seminars.

Extracurricular activities:

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Coursebooks:

Main coursebooks:

1. Andreas D. Baxevanis, B. F. Francis Ouellette: Bioinformatics - A Practical Guide to the Analysis of Genes and Proteins, John Wiley and Sons, 2005.

Supplementary coursebooks:

1. Current Protocols in Bioinformatics, John Wiley and Sons, 2007.
2. Arthur M. Lesk: Introduction to Bioinformatics, Oxford University Press, 2002.
3. Jonathan Pevsner: Bioinformatics and Functional Genomics, John Wiley and Sons, 2003.

Additional material:

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Lectures:

10 points (1 hour a week)

Syllabus:

• Bioinformatics and internet .
• NCBI data model.
• Databanks of gene sequences.
• Databanks of the protein structures.
• Maps of the gene in the genome.
• Extraction of information from the databanks using the Entrez system.
• Search of a databank, and the comparison of sequences.
• Creation and analysis of multiple alignments of the sequences of proteins.
• Prediction of the structure of the gene based on DNA sequence.
• Prediction of protein structure based on the protein sequences.
• Using cDNA sequence (EST) for the detection of protein-coding DNA sequences.
• The map of the human genome.
• Comparative analysis behind genome.
• Phylogenetic analysis of genome.

Exercises:

10 points (3 hours a week)

Syllabus:

• Searching for information on the Internet.
• NCBI, EBI - search of gene sequences.
• Uniprot search of protein sequences.
• Examples of practical use of internet resources for mapping the genome.
• Entrez system.
• FASTA program for comparing protein sequences.
• BLAST program for comparing protein sequences.
• CLUSTAL V and PSI-BLAST programs for the prediction of protein function based on multiple sequence comparisons.
• Auxiliary programs (ALSKRIPT, AMAS, Jal View) when a multiple alignment of the sequences of proteins.
• Locating protein-coding DNA sequences using GENESKAN and MZEF program.
• Prediction of the physico-chemical properties of the protein using ExPASy system (pI values of molecular weight, peptide maps, hydrophobicity).
• Forecast of the secondary structure of proteins using the program PREDATOR, PSIPRED and COILS.
• Phylogenetic analysis by PHILIP PhiloBLAST.
• Using the computer program (Vector NTI) in the design of the PCR primers, restriction analyzes and DNA cloning.

Semester papers:

20 points

Written exam:

60 points