david mount - diunitobotta/didattica/aa1112/introbioinfo.pdf · 2011. 10. 3. · computational...
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David MountBioinformatics: Sequence and Genome Analysis 2nd Edition
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Jin XiongEssential Bioinformatics
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Jones & PevznerBioinformatics Algorithms
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Baldi & BrunakBioinformatics: The Machine Learning Approach
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Higgins & TaylorBioinformatics: Sequence, Structure & Databanks
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NCBI Handbookhttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook
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NCBI Handbookhttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook
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EMBL-EBI Home Pagehttp://www.ebi.ac.uk/
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Berg, Tymoczko & StryerBiochemistry, Fifth Edition
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Genomics, Bioinformatics &Computational Biology
Computational Biology
Computational Molecular Biology
BioinformaticsGenomics
ProteomicsStructural Genomics
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DatabasesMachine Learning
Robotics
Statistics & ProbabilityArtificial Intelligence
Graph Theory
Information Theory
Algorithms
Genomics, Bioinformatics &Computational Biology
Computational Biology
Computational Molecular Biology
BioinformaticsGenomics
ProteomicsStructural Genomics
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What is Bioinformatics?
RNA Protein
DNA Phenotype
SelectionEvolution
Individuals
Populations
Biological Information
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Computational Goals of Bioinformatics
• Learn & Generalize: Discover conserved patterns (models) of sequences, structures, interactions, metabolism & chemistries from well-studied examples.
• Prediction: Infer function or structure of newly sequenced genes, genomes, proteins or proteomes from these generalizations.
• Organize & Integrate: Develop a systematic and genomic approach to molecular interactions, metabolism, cell signaling, gene expression…
• Simulate: Model gene expression, gene regulation, protein folding, protein-protein interaction, protein-ligand binding, catalytic function, metabolism…
• Engineer: Construct novel organisms or novel functions or novel regulation of genes and proteins.
• Gene Therapy: Target specific genes, or mutations, RNAi to change a disease phenotype.
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Central Paradigm of Molecular Biology
DNA RNA ProteinPhenotype
(Symptoms)
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Molecular Biology of the Gene 1965
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Challenges Understanding Genetic Information
GeneticInformation
MolecularStructure
BiochemicalFunction Phenotype
• Genetic information is redundant
• Structural information is redundant
• Genes and proteins are meta-stable
• Single genes have multiple functions
• Genes are one dimensional but function depends on three-dimensional structure
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Redundancy in Genomic& Protein Sequences
• DNA is double-stranded• Genetic code• Acceptable amino-acid
replacements• Intron-exon variation
• Alternative splicing• Strain variations (SNPs)
• Sequencing errors