C) PROGRAM:


Historical notes on the birth and evolution of Bioinformatics; purpose of Bioinformatics; examples of applications of bioinformatics tools in biological investigations. Components of a computer: hardware and software; Internet; World Wide Web; Communication protocols.
Educational objective 2)
Databases: general characteristics, historical notes, classification, acquisition and storage of data, management systems, query languages. NCBI-Entrez, SIB-Expasy and EBI-SRS; Pubmed; Primary databases of nucleotide sequences: GenBank, EMBL nucleotide database. Primary databases of protein sequences: UniPROT. Primary databases of protein structures: Protein Data Bank. Secondary databases: SCOP, CATH, ProDOM, PROSITE. Specialized databases: STRING, GENECARDS, GENOMIC BROWSERS, MODEL ORGANISM DATABASE. Gene Ontology analysis: AmiGO database. Multiorganism expression database: GeneVestigator. System Biology databases: MapMAN, Panther, ePlant database.
Training objective 3)
Sequence similarity research: purpose and importance. Dot matrix. Replacement matrices (PAM, BLOSUM). Needleman-Wunsch algorithm. Smith-Waterman algorithm. Heuristic alignment algorithms. Tool to search for sequence similarities: FASTA, BLAST. Single alignments: LALIGN. Multiple alignments: Clustal and T-Coffee.
Learning objective 4)
From the sequence to the structure of a protein: general description of the experimental and computational approaches. Protein secondary structure prediction: statistical methods (Chou and Fasman; Garnier, Osguthorpe and Robson) and connection methods (PHD sec). Tertiary structure prediction: homology modeling (skeleton modeling, loops and side chains) and use of Swiss Model. Prediction of the function of a protein: analysis of surface topography (CastP), research of structural motifs (evolutionary trace), research of protein-protein interaction sites (SPPIDER). CASP and CAPRI project. Functional in silico characterization of genes and proteins: use of the main tools.
Educational objective 5)
4) Genome wide association study: introduction, development, potential. GWA study: AMM algorithm, use of GWAPP, description of a case study. How to carry out a GWA study using GWAPP, using a dataset relating to the HapMap collection of Arabidopsis. Metagenomics and amplicon sequencing: introduction, development, potential. RNA-Seq: potential, description of the technique and bioinformatics tools for data analysis.

Practical exercises will be conducted entirely in English on the topics of objectives 2,3,4,5 for a total of 1 ECTS. In addition, the topics of Objectives 2 and 5 will be carried out entirely in English.

S.Pascarella, A.Paiardini. Bioinformatica, dalla sequenza alla struttura delle proteine. Ed. Zanichelli
-A. Tramontano. Bioinformatica. Ed. Zanichelli

Materiali distribuiti durante il corso (presentazioni ppt, articoli scientifici)