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

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Alternative Splicing Generates DistinctProteinsPromoterExon Intron Exon Intron Exon TerminatorGeneTranscriptSplicingCappoly-A5’ 3’mRNA-1Alternate SplicingTranscriptCappoly-A5’ 3’mRNA-2
ESTs, Full Length cDNAUniGene & RefSeq DatabasesPromoterExon Intron Exon Intron Exon Terminator5’ UTR3’ UTRGeneSplicingTranscriptCappoly-A5’ 3’5’ ESTsmRNA3’ ESTs5’ UTR 3’ UTRProteinFull Length cDNA
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BioinformaticsGenomics& Medicinehtt
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Computational Goals of Bioinformati
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Central Paradigm of MedicineDNA RNA
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Soybean Leghemoglobin andSperm Whal
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Challenges Understanding Genetic In
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Dayhoff’s PAM 250Amino Acid Repla
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Discovering Function from Protein S
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A Typical Motif:Zinc Finger DNA Bin
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Position-Specifc Scoring Matrix for
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Blocks or Finger Prints fromMultipl
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Hidden Markov Models fromMultiple S
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Data Mining:The Seach for Buried Tr
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PROSITE Patternshttp://expasy.org/p
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Expasy Bioinformatics Resource Port
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UniProt Knowledge Basehttp://www.un
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UniProt Human Opsin Advanced Search
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UniProt Human Opsin OPN1MW Entryhtt
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Blast UniProt Human OPN1MW Resultsh
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NCBI BLAST Home Pagehttp://blast.nc
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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
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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
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Page 111: pFAM at Sanger Center (UK)http://pf
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