bioinformatics searching sequence databases

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1、Bioinformatics:SearchingSequenceDatabasesandtheFutureofBioinformaticsLauriePepperMPSThesisApril27,2001IntroductionBioinformatics:Thescienceoforganizingandanalyzingdata.MolecularBiologyHumanGenomeProjectDataToolsSearchalgorithmsDatabasesBioinformaticsWhyt

2、hisfieldisimportantAmountofdataSearchingBioinformaticsGenomics:DNAandRNAProteomics:ProteinstructureandfunctionNeuroinformatics:BrainstructureandcompositionMolecularBiologyDNAandRNABasesStructureProteinAminoAcidsStructureMolecularBiologyDNA/RNAandproteinsc

3、anbereadas“strings”.Examples:ATCGCC(DNA)UGACUU(RNA)ACGHILMPST(Protein)MolecularBiologyGenes-WhytheyareimportantEvolutionProteins-GeneproductsDotheworkoflifeWhatwewanttodowithbioinformaticsAlgorithmsTimeExactmatchingFinding‘ABCD’in‘AABCDABBCCD’Inexactmatch

4、ingFinding‘ABCD’in‘ABBCDDAFBCD’MultiplestringcomparisonComputersandProgramsDatabasesSearchtoolsSubstitutionmatricesPairwisesequencecomparisonMultiplesequencecomparisonDatabasesPrivatevs.PublicPublicDNA/RNAGenBankProteinSwiss-ProtPROSITESearchProgramsPairw

5、iseSequenceAlignmentBLASTFASTAMultipleSequenceAlignmentCLUSTALWSubstitutionMatricesSubstitutionMatricesDayhoff/PAMBLOSUMSubstitutionMatrices:SimplifiedThehigherthescore,thebetteramatchis.Example:A-->A=3A-->B=1A-->C=0A-->D=-3Match1:AAAAABABScore:3+1+3+1=8-

6、--------------------------Match2:AAAAABADScore:3+1+3+(-3)=4TheFutureBiologyEthical,LegalandSocialImplicationsHumanGenomeProjectFunctionalGenomicsMedicineComputerScienceAlgorithmsSearchAlgorithmsSequenceVariationAlgorithmsReferencesDNAhelix:http://www.ornl

7、.gov/TechResources/Human_Genome/publicat/primer/fig1.htmlGenBankgraph:http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.htmlBLOSUM62matrix:http://www.blc.arizona.edu/courses/bioinformatics/blosum.htmlAcknowledgementsProfessorC.ShilepskyProfessorCollmerMPSm

8、ajorsMyfamilyAnyQuestions?