The teaching is organized as follows:

Learning outcomes

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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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The course will provide the theoretical and practical basis to understand and employ algorithms and programs currently used in Bioinformatics. Major biological databases will be introduced with a special focus on genomic, proteomic and biochemical information. The students will also be introduced to the most modern fields of structural bioinformatics and systems biology.

Program

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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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Theoretical Module - Overview of the main structural features of proteins and nucleic acids in relation to the concept of evolution. Introduction to biomolecular databases: online resources and their use - Biological databases: organization and integration of information concerning: a) protein and nucleic acid sequences; b) biomolecular structures; c) bibliographic and scientific literature. Retrieve of specific information: use of limitations and Boolean operators. - Sequence comparison and alignments: static and dynamic algorithms; substitution matrices (PAM,BLOSUM) - - Search-algorithms: FASTA and BLAST; Smith-Waterman; Needleman-Wunsch; statistic significance for an alignment (z-score, expectation values and probability) - Multiple sequence alignments: ClustalW, search on specific databases, other algorithms, PSI-BLAST - Short introduction on philogenetic trees - Introduction to Structural Bioinformatics: visualization and analysis of protein and nucleic acid 3D structures - Methods to predict protein secondary structure elements starting from the sequence - Introduction to Systems Biology: Spatial and temporal scales, static and dynamic models, mathematical frameworks, introduction on signal transduction networks Laboratory Module - Introduction to Linux - NCBI databases: Entrez interface, Gene, UniGene, Protein, Uniprot and EBI - Single and multiple sequence alignments, score matrices, optimal methods; online resources and spreadsheets - BLAST,PSI-BLAST and BLAT: online tools and their use - Tools for multiple alignments, the Homologene databank, computation and visualization of multiple alignments - Tools for phylogenesis : Mobyle (Institut Pasteur and Phylogeny.fr) - Introduction to PyMol and molecular visualization. Use of PSI-PRED and JPRED for predicting secondary structures from sequences - Systems biology: numerical simulation of simple biochemical reactions. Building simple kinetic models by using SBOTOOLBOX2 for Matlab; application to G-potein signalling cycles.

Bibliography

Examination Methods

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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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Written exam for both modules. The two marks will be averaged. Students can chose to prepare a presentation in groups of 3-4 students on a selected database, which will also contribute to the final mark. An oral examination can be chose in addition, in order to improve the final mark.