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

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Challenges Understanding Genetic InformationGeneticInformationMolecularStructureBiochemicalFunctionPhenotype• Genetic information is redundant• Structural information is redundant• Genes and proteins are one dimensional buttheir function depends on three-dimensionalstructure
Challenges Understanding Genetic InformationGeneticInformationMolecularStructureBiochemicalFunctionPhenotype• Genetic information is redundant• Structural information is redundant• Genes and proteins are one dimensional buttheir function depends on three-dimensionalstructure• Genes and proteins are meta-stable
Page 1 and 2: BioinformaticsGenomics& Medicinehtt
Page 3 and 4: Computational Goals of Bioinformati
Page 5 and 6: Central Paradigm of MedicineDNA RNA
Page 9: Soybean Leghemoglobin andSperm Whal
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
Page 53 and 54: BLAST Conserved Domain Output
Page 55 and 56: Most Signifcant Similarity Hits
Page 57 and 58: Bovine Blue Opsin Similarity
Page 59 and 60: Evaluation of ProflesNegative Prote
Page 61 and 62:
MyHits Local Motifs Searchhttp://my
Page 63 and 64:
MyHits Local Motifs Searchhttp://my
Page 65 and 66:
MyHits Local Motif Hitshttp://myhit
Page 67 and 68:
MyHits Local Motifs Hist (Cont.)
Page 69 and 70:
InterProhttp://www.ebi.ac.uk/interp
Page 71 and 72:
InterPro Scanhttp://www.ebi.ac.uk/T
Page 73 and 74:
InterPro Scan Resultshttp://www.ebi
Page 75 and 76:
GO: Gene Ontology Databasehttp://ww
Page 77 and 78:
GO: Gene Ontology for Opsin OPN1MWh
Page 79 and 80:
GO: Annotations for OPN1MWhttp://ww
Page 81 and 82:
GO: Gene Ontology Terms for OPN1MWh
Page 83 and 84:
GO: Gene Ontology GCPR Termhttp://w
Page 85 and 86:
Bioinformatics Homeworkhttp://bioch
Page 87 and 88:
Statistical vs. Biological Signifca
Page 89 and 90:
Hidden Markov Models fromMultiple S
Page 91 and 92:
Structure of 5’ CAP© Michael W.
Page 93 and 94:
Intron Splicing Mechanism© Michael
Page 95 and 96:
GENSCAN Gene Modelhttp://genes.mit.
Page 97 and 98:
ESTs, Full Length cDNAUniGene & Ref
Page 99 and 100:
HiddenMarkov modelsof genestructure
Page 101 and 102:
Genomics, Bioinformatics &Computati
Page 103 and 104:
Genomics, Bioinformatics &Computati
Page 105 and 106:
Hidden Markov Models (after Haussle
Page 107 and 108:
pFAM at Sanger Center (UK)http://pf
Page 109 and 110:
Page 111:
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