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Programma
Introduzione: sequenze e strutture, gestione e analisi dei dati, dogma centrale, storia evolutiva delle sequenze, genoma. Evoluzione di DNA e proteine: Teoria neutrale, omologia, ortologia, paralogia, somiglianza, metriche per il confronto sequenze, PAM, divergenza, orologio molecolare, Ks, Ka, evoluzione accelerata, evoluzione convergente. Predizioni biochimiche: proprieta biochimiche prevedibili, motivi e segnali, evoluzione convergente di motivi, Prosite, ricerca di patterns, segnali di degradazione, PEST, protein sorting, sequenze segnale, sequenze di ancoraggio, glicosilazione, fosforilazione, ProtParam. Struttura di RNA e proteine: Tipi di strutture secondarie dell'RNA, hairpin, bulge, loop, pseudoknots, Minimum free energy, stacking energy, analisi di covarianza, predizione di strutture secondarie,PHD, accessibilita al solvente, classi, architetture, fold, CATH, SCOP, homology modelling, threading, Coiled coils, proteine di membrana, topologia transmembrana. Allineamento a coppie: allineamento combinatoriale, Dot plots, sequenze ripetute, algoritmo, programmazione dinamica, Needleman-Wunsh, Smith-W! aterman, ga p penalty, significativita. Allineamento multiplo: Usi dell'allineamento multiplo, MSA, Allineamento progressivo, CLUSTALW, Allineamento iterativo, PRRP, BAliBASE, profili, hidden markov models, profili HMM, Pfam, Sequence logos. Banche Dati e ricerca di omologia: entry, GenBank, SwissProt, PDB, Expressed Sequence Tags, IMAGE, SRS, Entrez, FASTA, BLAST, PSI-BLAST, significativita, sensibilita, selettivita, copertura. Analisi filogenetica: tree of life, nomenclatura degli alberi filogenetici, cladogrammi, filogrammi, alberi ultrametrici, alberi rooted e unrooted, distanze aminoacidiche e nucleotidiche, UPGMA, Neighbour-joining, maximum likelihood, parsimonia, bootstrap. Genomi: mappe fisiche e mappe genetiche, DNA fingerprinting, BAC, metodi di sequenziamento genomico: ?clone by clone? e WGS, assemblaggio, contig, scaffold, sequenze draft e finished, ORF, gene-finding. G! enomica com parativa. Associazioni funzionali tra proteine dedotte da genomi completi.
Introduction: sequences and structures, data management and analysis, central dogma, evolutionary history of sequences and genome. Evolution of DNA and proteins: Neutral theory, homology, orthology, paralogy, similarity, metrics for sequence comparison, PAM, divergence, molecular clock, Ks, Ka, accelerated evolution, convergent evolution. Biochemical predictions: predictable biochemical properties, patterns and signals, convergent evolution of patterns, Prosite, search for patterns, degradation signals, PEST, protein sorting, signal sequences, anchor sequences, glycosylation, phosphorylation, ProtParam. Structure of RNA and proteins: Types of secondary RNA structures, hairpin, bulge, loop, pseudoknots, Minimum free energy, stacking energy, covariance analysis, prediction of secondary structures, PHD, accessibility to solvent, classes, architecture, fold, CATH, SCOP, homology modelling, threading, Coiled coils, membrane proteins, transmembrane topology. Pairwise alignment: combinatorial alignment, Dot plots, repeated sequences, algorithm, dynamic programming, Needleman-Wunsh, Smith-Waterman, gap penalty, significance. Multiple alignment: Uses of multiple alignment, MSA, progressive alignment, CLUSTALW, iterative alignment, PRRP, BAliBASE, profiles, hidden Markov models, HMM profiles, Pfam, Sequence logos. Databases and search for homology: entry, GenBank, SwissProt, PDB, Expressed Sequence Tags, IMAGE, SRS, Entrez, FASTA, BLAST, PSI-BLAST, significance, sensitivity, selectivity, coverage. Phylogenetic analysis: tree of life, nomenclature of phylogenetic trees, cladograms, phylograms, ultrametric trees, rooted and unrooted trees, amino acid and nucleotide distances, UPGMA, Neighbour-joining, maximum likelihood, parsimony, bootstrap. Genomes: physical maps and genetic maps, DNA fingerprinting, BAC, genomic sequencing methods: clone by clone and WGS, assembly, contig, scaffold, draft and finished sequences, ORF, gene-finding. Comparative genomics. Functional associations between proteins inferred from complete genomes.
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Attiva
