Databases and Comparisons - CMB Education - Karolinska Institutet

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Docking of bile acids into class I γγ ADHLinköping University & Karolinska Institutet 12
Docking of bile acids into class I γγ ADH2.19Distances in Å at active siteγγ-ADH48(Og)--Ho3Zn--O3C4(NAD)--H3isoUDCA 2.22 2.30 2.19UDCA 3.20 2.88 3.532.22ββ-ADHisoUDCA 3.35 2.24 1.94UDCA 2.31 2.51 2.942.30ADH=alcohol dehydrogenaseUDCA=ursodeoxycholic acidLinköping University & Karolinska Institutet 13
Page 1 and 2: Introduction to BioinformaticsDatab
Page 3 and 4: Genome comparisons
Page 5 and 6: Completed genomesGenome sizeMb10000
Page 7 and 8: Genome comparisonsH. sapienscluster
Page 9 and 10: Protein foldingDNAProtein?Linköpin
Page 11: Molecular modellingHomology modelli
Page 15 and 16: Predictions of important regionsCom
Page 17 and 18: Conserved amino acid residuesLinkö
Page 19 and 20: Databases with sequence information
Page 21 and 22: Example of Swissprot entryID 2BHD_S
Page 23 and 24: TrEMBLA computer-annotated suppleme
Page 25 and 26: Example of EMBL entryID HS3B5H5E st
Page 27 and 28: Example of EMBL entry, cont.FT CDS
Page 29 and 30: Example of PDB entryHEADER OXIDORED
Page 31 and 32: Example of PDB entry, cont.SEQRES 1
Page 33 and 34: Pairwise sequence comparisons
Page 35 and 36: Why comparisons?Identification of p
Page 37 and 38: Results from diagonal plot analysis
Page 39 and 40: Improved comparisons 1Not just cons
Page 41 and 42: Selection of scoring matrixThe scor
Page 43 and 44: Using scoring matrixS 0 0 0 0 0=4C
Page 45 and 46: PAM, cont.The PAM series are based
Page 47 and 48: BLOSUMOne assumption inherent in th
Page 49 and 50: Improved comparisons 2Introduction
Page 51 and 52: Gap penaltyThe score from all pairs
Page 53 and 54: Lipman & PearsonFASTAIdentities / S
Page 55 and 56: Results from FASTA run, histogramop
Page 57 and 58: Results from FASTA run, alignment>>
Page 59 and 60: Caution with the interpretationsAn
Page 61 and 62: EBI home pageLinköping University
Page 63 and 64:
http://www.ebi.ac.uk/fasta33/Linkö
Page 65 and 66:
BLASTFast algorithmLocal installati
Page 67 and 68:
NCBI home pageLinköping University
Page 69 and 70:
Basic BLASTLinköping University &
Page 71 and 72:
Basic BLAST, resultsLinköping Univ
Page 73 and 74:
FASTA parametersScoring matrix- BLO
Page 75 and 76:
Statistics, high penalties (48, 8)L
Page 77 and 78:
Effect on alignment by gap penaltie
Page 79 and 80:
Multiple sequence alignmentsCharact
Page 81 and 82:
Clustering + AligningClustalAll-aga
Page 83 and 84:
ClustalW main menu****************
Page 85 and 86:
Pairwise alignment parameters******
Page 87 and 88:
ClustalW at EBI, Submission formLin
Page 89 and 90:
waiting ...Linköping University &
Page 91 and 92:
ClustalW, Scores TableLinköping Un
Page 93 and 94:
ClustalW, Guide Tree & CladogramLin
Page 95 and 96:
JalViewA new experimental option ha
Page 97 and 98:
Sequence formats in ClustalW Pearso
Page 99 and 100:
Kalign, AlignmentLinköping Univers
Page 101 and 102:
PSI-BLASTQuery sequenceFound homolo
Page 103 and 104:
PSI-BLAST, resultsLinköping Univer
Page 105 and 106:
Expect valuesThe first of these (up
Page 107 and 108:
Advanced OptionsIn the "Advanced Op
Page 109 and 110:
Set the output formatting optionsBy
Page 111 and 112:
Output from initial BLAST searchThe
Page 113 and 114:
Examination, cont.Sequences produci
Page 115 and 116:
Examination, cont.sp|P42297|YXIE_BA
Page 117 and 118:
Performing PSI-BLAST iterationsThe
Page 119:
Assignment 1Sequence comparisons- F
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