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Fundamentals of Bioinformatics 6
Module PRINCIPLES OF BIOINFORMATICS

Academic Year 2024/2025 - Teacher: FRANCESCA MARIA GUARINO

Expected Learning Outcomes

 With the teaching of PRINCIPLES OF BIOINFORMATICS, the necessary tools will be provided in order to enable students to acquire the understanding and progression of scientific knowledge in the field of biology of the macromolecules through the potential and applications of Bioinformatics. Furthermore, knowledge of the biological principles underlying the functioning of bioinformatics software, their characteristics and limitations will be imparted. The student will be able, at the end of the course, to use the bioinformatics analysis tools available on the web in order to study and to analyze biological macromolecules for experimental design in the field of biotechnological research and industrial production.

Course Structure

The lessons will consist of PowerPoint presentations. Online exercises and demonstrations will also be performed with the most popular bioinformatics websites. In the exercises, students will be asked to carry out simple exercises on the topics covered.

Required Prerequisites

At least high school level knowledge of the main basic topics of molecular biology and computer science would be useful

Attendance of Lessons

Attendance considered compulsory for the course of study

Detailed Course Content

OUTLINES OF MOLECULAR BIOLOGY. Structure of biological macromolecules. Chemical-physical properties of nucleic acids. The structure, topology and conformation of the DNA double helix. The structure, classes of RNA and their functional versatility. Basics of protein structure. Organization and physical and functional characteristics of the genomes of prokaryotes and eukaryotes. Organization of DNA in the cell and chromatin structure. Structure and function of genes. Meaning of coding and non-coding sequences in the genome. Notes on the molecular mechanisms of biological macromolecules: replication, transcription and translation. Central dogma of biology and its modifications: point mutations, nonsense mutations and missense mutations, genetic code degeneration.  BIOINFORMATICS. Primary and secondary databases. Organization of entries in databases. NCBI and EMBL and the Entrez and SRS retrieval systems. Principles of sequence alignment techniques. Concept of homology and similarity. Assignment of scoring to an alignment of sequences using PAM and BLOSUM matrices. Sequence alignment methods: dot matrix method, exhaustive and heuristic algorithms. Global and local sequence alignment programs. Biological meaning of alignment. Alignment programs for BD screening: FASTA and BLAST. A measure of the statistical significance of an alignment. Biological significance of multialignment. Sequence multialignment methods and programs: ClustalW/Ω program, T-coffe. Definition and meaning of protein functional motifs: consensus sequences, patterns and profiles.

Textbook Information

Stefano Pascarella, Alessandro Paiardini.  Bioinformatica-Dalla sequenza alla struttura delle proteine- Zanichelli 2011

Manuela Helmer Citterich, Fabrizio Ferrè, Giulio Pavesi, Graziano Pesole, Chiara Romualdi.  Fondamenti di bioinformatica.  Zanichelli  2018

Course Planning

 SubjectsText References
1Structure of macromolecules: DNA, RNA, proteinsS. Pascarella, et al.  Bioinformatica-Dalla sequenza alla struttura delle proteine- Zanichelli 2011
2Organization of genomes and genesS. Pascarella, et al.  Bioinformatica-Dalla sequenza alla struttura delle proteine- Zanichelli 2011
3Central dogma of molecular biologyS. Pascarella, et al.  Bioinformatica-Dalla sequenza alla struttura delle proteine- Zanichelli 2011
4Genetic code and mutationsS. Pascarella, et al.  Bioinformatica-Dalla sequenza alla struttura delle proteine- Zanichelli 2011
5Biological databasesM. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018
6Sequence alignmentsM. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018
7 Alignment and scoring methods M. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018
8PAM and BLOSUM matricesM. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018
9BLAST alignment programsM. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018
10Clustal multialignment programsM. Helmer Citterich, et al.  Fondamenti di bioinformatica.  Zanichelli  2018

Learning Assessment

Learning Assessment Procedures

written test and oral interview

Information for students with disabilities and/or DSA

To guarantee equal opportunities and in compliance with current laws, interested students can request a personal interview in order to plan any compensatory and/or dispensatory measures, based on the educational objectives and specific needs. It is also possible to contact the CInAP representative (Centre for Active and Participatory Integration - Services for Disabilities and/or DSA) of the Department of Biomedical and Biotechnological Sciences.

Examples of frequently asked questions and / or exercises

What are primary biological databases and how are they constructed?

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