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1、CHAPTER1HistoricalIntroductionandOverviewThefirstsequencestobecollectedwerethoseofproteins,2DNAsequencedatabases,3Sequenceretrievalfrompublicdatabases,4Sequenceanalysisprograms,5Thedotmatrixordiagrammethodforcomparingsequences,5Alignmentofsequencesbydynamicprogramming,6Fi
2、ndinglocalalignmentsbetweensequences,8Multiplesequencealignment,9PredictionofRNAsecondarystructure,9Discoveryofevolutionaryrelationshipsusingsequences,10Importanceofdatabasesearchesforsimilarsequences,11TheFASTAandBLASTmethodsfordatabasesearches,11Predictingthesequenceofa
3、proteinbytranslationofDNAsequences,12Predictingproteinsecondarystructure,13Thefirstcompletegenomesequence,14ACEDB,thefirstgenomedatabase,15REFERENCES,1512■CHAPTER1THEDEVELOPMENTOFSEQUENCEANALYSISMETHODShasdependedonthecontributionsofmanyindividualsfromvariedscientificback
4、grounds.Thischapterprovidesabriefhistor-icalaccountofthemoresignificantadvancesthathavetakenplace,aswellasanoverviewofthechaptersofthisbook.Becausemanycontributorscannotbementionedduetospaceconstraints,additionalreferencestoearlierandcurrentreferencebooks,articles,reviews
5、,andjournalsprovideabroaderviewofthefieldandareincludedinthereferenceliststothischapter.THEFIRSTSEQUENCESTOBECOLLECTEDWERETHOSEOFPROTEINSThedevelopmentofprotein-sequencingmethods(SangerandTuppy1951)ledtothesequencingofrepresentativesofseveralofthemorecommonproteinfamilies
6、suchascytochromesfromavarietyoforganisms.MargaretDayhoff(1972,1978)andhercollabo-ratorsattheNationalBiomedicalResearchFoundation(NBRF),Washington,DC,werethefirsttoassembledatabasesofthesesequencesintoaproteinsequenceatlasinthe1960s,andtheircollectioncentereventuallybecame
7、knownastheProteinInformationResource(PIR,formerlyProteinIdentificationResource;http://watson.gmu.edu:8080/pirwww/index.html).TheNBRFmaintainedthedatabasefrom1984,andin1988,thePIR-InternationalMargaretDayhoffProteinSequenceDatabase(http://www-nbrf.georgetown.edu/pir)wasest
8、ablishedasacollaborationofNBRF,theMunichCenterforProteinSequences(MIPS),andtheJapanInternational
