Fundamentals of Bioinformatics 2

Module PRINCIPLES OF BIOINFORMATICS

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 biological 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 and students will be given the ability to use the most popular tools available on the web.  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.

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.

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

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.