- Page 1: Introduction to BioinformaticsDatab
- Page 5 and 6: Completed genomesGenome sizeMb10000
- Page 7 and 8: Genome comparisonsH. sapienscluster
- Page 9 and 10: Protein foldingDNAProtein?Linköpin
- Page 11 and 12: Molecular modellingHomology modelli
- Page 13 and 14: Docking of bile acids into class I
- 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
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BLASTFast algorithmLocal installati
- Page 67 and 68:
NCBI home pageLinköping University
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Basic BLASTLinköping University &
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Basic BLAST, resultsLinköping Univ
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FASTA parametersScoring matrix- BLO
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Statistics, high penalties (48, 8)L
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Effect on alignment by gap penaltie
- Page 79 and 80:
Multiple sequence alignmentsCharact
- Page 81 and 82:
Clustering + AligningClustalAll-aga
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ClustalW main menu****************
- Page 85 and 86:
Pairwise alignment parameters******
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ClustalW at EBI, Submission formLin
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waiting ...Linköping University &
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ClustalW, Scores TableLinköping Un
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ClustalW, Guide Tree & CladogramLin
- Page 95 and 96:
JalViewA new experimental option ha
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Sequence formats in ClustalW Pearso
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Kalign, AlignmentLinköping Univers
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PSI-BLASTQuery sequenceFound homolo
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PSI-BLAST, resultsLinköping Univer
- Page 105 and 106:
Expect valuesThe first of these (up
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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
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Examination, cont.sp|P42297|YXIE_BA
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Performing PSI-BLAST iterationsThe
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Assignment 1Sequence comparisons- F