Teacher
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PROIETTI Silvia
(syllabus)
Training objective 1) History of Bioinformatics; goals of Bioinformatics; examples of applications of bioinformatics tools in Biology Research. Computer components: hardware and software; Internet; World Wide Web; Communication protocols.
Training objective 2) Biological Databases: general features, historical information, classification, data capture and storage, 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 database for protein structures: Protein Data Bank. Secondary databases: SCOP, CATH, ProDOM, PROSITE. Specialized database: STRING, GENECARDS, GENOMIC BROWSERS, MODEL ORGANISM DATABASE. Gene Ontology Analysis: AmiGO Database. Multiorganism expression database: GeneVestigator. System Biology databases: MapMAN, Panther, and ePlant database.
Training objective 3) Sequence similarity searches: goal and relevance. Dot matrix. Substitution Matrices (PAM, BLOSUM). Needleman-Wunsch Algorithm. Smith-Waterman Algorithm. Heuristic alignment algorithms. Sequence similarity search tools: FASTA, BLAST. Local alignments: LALIGN. Multiple alignments: Clustal and T-Coffee.
Training objective 4) From the sequence to the structure of a protein: general description of experimental and computational approaches. Prediction of secondary structure of proteins: statistical methods (Chou and Fasman, Garnier, Osguthorpe and Robson) and neural networks (PHD sec). 3D structure prediction: homology modeling (scaffold, loop and side chains modeling). Swiss Model. Protein function prediction: Surface Topography Analysis (CastP), Structural motifs search: Evolutionary Trace, Protein-Protein Interaction site search (SPPIDER). CASP and CAPRI project. In silico functional and structural characterization of genes and proteins: use of the main tools.
Training objective 5) Genome wide association study: introduction, development, potential. GWA Study: AMM algorithm, use of GWAPP, description of a "case-study". How to perform a GWA study using GWAPP using a dataset related to the HapMap collection of Arabidopsis. Metagenomics and amplicon sequencing: Introduction, Development, Potential. RNA-Seq: Potential, description of technique and bioinformatics tools for data analysis.
Practical lessons will be given on training objectives 2,3,4,5 for a total of 1 CFU. Moreover, topics of objectives 2 and 5 will be teached in English.
(reference books)
-S.Pascarella, A.Paiardini. Bioinformatica, dalla sequenza alla struttura delle proteine. Ed. Zanichelli -Citterich et al. Fondamenti di bioinformatica. Ed. Zanichelli, 2018 -A. Tramontano. Bioinformatica. Ed. Zanichelli
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