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1、CHAPTER1HistoricalIntroductionandOverviewThefirstsequencestobecollectedwerethoseofproteins,2DNAsequencedatabases,3Sequenceretrievalfrompublicdatabases,4Sequenceanalysisprograms,5Thedotmatrixordiagrammethodforcomparingsequences,5Alignmentofsequencesbydynamicprogramming,6Findinglocalalignme
2、ntsbetweensequences,8Multiplesequencealignment,9PredictionofRNAsecondarystructure,9Discoveryofevolutionaryrelationshipsusingsequences,10Importanceofdatabasesearchesforsimilarsequences,11TheFASTAandBLASTmethodsfordatabasesearches,11PredictingthesequenceofaproteinbytranslationofDNAsequences
3、,12Predictingproteinsecondarystructure,13Thefirstcompletegenomesequence,14ACEDB,thefirstgenomedatabase,15REFERENCES,1512■CHAPTER1THEDEVELOPMENTOFSEQUENCEANALYSISMETHODShasdependedonthecontributionsofmanyindividualsfromvariedscientificbackgrounds.Thischapterprovidesabriefhistor-icalaccount
4、ofthemoresignificantadvancesthathavetakenplace,aswellasanoverviewofthechaptersofthisbook.Becausemanycontributorscannotbementionedduetospaceconstraints,additionalreferencestoearlierandcurrentreferencebooks,articles,reviews,andjournalsprovideabroaderviewofthefieldandareincludedinthereferenc
5、eliststothischapter.THEFIRSTSEQUENCESTOBECOLLECTEDWERETHOSEOFPROTEINSThedevelopmentofprotein-sequencingmethods(SangerandTuppy1951)ledtothesequencingofrepresentativesofseveralofthemorecommonproteinfamiliessuchascytochromesfromavarietyoforganisms.MargaretDayhoff(1972,1978)andhercollabo-rato
6、rsattheNationalBiomedicalResearchFoundation(NBRF),Washington,DC,werethefirsttoassembledatabasesofthesesequencesintoaproteinsequenceatlasinthe1960s,andtheircollectioncentereventuallybecameknownastheProteinInformationResource(PIR,formerlyProteinIdentificationResource;http://watson.gmu.edu:8
7、080/pirwww/index.html).TheNBRFmaintainedthedatabasefrom1984,andin1988,thePIR-InternationalMargaretDayhoffProteinSequenceDatabase(http://www-nbrf.georgetown.edu/pir)wasestablishedasacollaborationofNBRF,theMunichCenterforProteinSequences(MIPS),andtheJapanInternational
