Bioinformatics Slides (PDF) - Genomics & Medicine - Stanford ...

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What is <strong>Bioinformatics</strong>?IndividualsRNAProteinDNAPhenotypeEvolutionSelectionPopulationsBiological Information
Computational Goals of <strong>Bioinformatics</strong>• Learn & Generalize: Discover conserved patterns (models) ofsequences, structures, metabolism & chemistries from well-studiedexamples.• Prediction: Infer function or structure of newly sequenced genes,genomes, proteomes or proteins from these generalizations.• Organize & Integrate: Develop a systematic and genomic approach tomolecular 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 novelregulation of genes and proteins.• Target: Mutations, RNAi to specifc genes and transcripts or drugs tospecifc protein targets.
Page 1: BioinformaticsGenomics& Medicinehtt
Page 5 and 6: Central Paradigm of MedicineDNA RNA
Page 9 and 10: Soybean Leghemoglobin andSperm Whal
Page 11 and 12: Challenges Understanding Genetic In
Page 13 and 14: Dayhoff’s PAM 250Amino Acid Repla
Page 15 and 16: Discovering Function from Protein S
Page 17 and 18: A Typical Motif:Zinc Finger DNA Bin
Page 21 and 22: Position-Specifc Scoring Matrix for
Page 23 and 24: Blocks or Finger Prints fromMultipl
Page 25 and 26: Hidden Markov Models fromMultiple S
Page 27 and 28: Data Mining:The Seach for Buried Tr
Page 29 and 30: PROSITE Patternshttp://expasy.org/p
Page 31 and 32: Expasy Bioinformatics Resource Port
Page 33 and 34: UniProt Knowledge Basehttp://www.un
Page 35 and 36: UniProt Human Opsin Advanced Search
Page 37 and 38: UniProt Human Opsin OPN1MW Entryhtt
Page 39 and 40: Blast UniProt Human OPN1MW Resultsh
Page 41 and 42: NCBI BLAST Home Pagehttp://blast.nc
Page 45 and 46: Entrez Gene search for Colorblindne
Page 47 and 48: Entrez Gene search for Opsins
Page 49 and 50: BLAST Similarity Searchhttp://www.n
Page 51 and 52: Paste Sequence, Choose SwissProt Da
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BLAST Conserved Domain Output
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Most Signifcant Similarity Hits
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Bovine Blue Opsin Similarity
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Evaluation of ProflesNegative Prote
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MyHits Local Motifs Searchhttp://my
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MyHits Local Motifs Searchhttp://my
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MyHits Local Motif Hitshttp://myhit
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MyHits Local Motifs Hist (Cont.)
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InterProhttp://www.ebi.ac.uk/interp
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InterPro Scanhttp://www.ebi.ac.uk/T
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InterPro Scan Resultshttp://www.ebi
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GO: Gene Ontology Databasehttp://ww
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GO: Gene Ontology for Opsin OPN1MWh
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GO: Annotations for OPN1MWhttp://ww
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GO: Gene Ontology Terms for OPN1MWh
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GO: Gene Ontology GCPR Termhttp://w
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Bioinformatics Homeworkhttp://bioch
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Statistical vs. Biological Signifca
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Hidden Markov Models fromMultiple S
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Structure of 5’ CAP© Michael W.
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Intron Splicing Mechanism© Michael
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GENSCAN Gene Modelhttp://genes.mit.
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ESTs, Full Length cDNAUniGene & Ref
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HiddenMarkov modelsof genestructure
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Genomics, Bioinformatics &Computati
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Genomics, Bioinformatics &Computati
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Hidden Markov Models (after Haussle
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pFAM at Sanger Center (UK)http://pf
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