蛋白质相互作用研究方法数据库系统的设计与实现

华中科技大学硕士学位论文蛋白质相互作用研究方法数据库系统的设计与实现姓名：舒小琴申请学位级别：硕士专业：生物信息学指导教师：刘曼西20060403ILinuxapacheMySQLPHPWebIIAbstractThestudyoftheproteomeisbecominganewhotspotafterthehumangenomeproject.Protein-Proteininteractionnetworkstudyisamainsubjectofthestudyoftheproteomefunctionmode.Throughrecentlytensyears’development,alargeamountofcorrelativeliteratureshavebeenappearedinmanyfamousmagazines,whiletheseliteraturesshowingtheirdataresults,theyalsoshowingtheirstudyprocesses,whichmaybetheimportantreferencesfortheafterwardstudiers.Duringthegeneralstudywork,themakingoftheexperimentprojecttraditionallyisthroughreadingandcomparinglotsofcorrelativeliteratures,andthencombiningthestudiers’experiencestocompletethisjob.Butnowsolargeamountofthereferencesmakethisjobalwayssodifficult.Thensuchkindsofexperimentsmethodsdatabasesaregreatlyneeded.Butuntilnow,thereisnosuchmethodsdatabase.Inthispaper,wecollectlotsofcorrelativereferenceliteraturesclassifythesestudymethodsusedinprotein-proteininteractionintothreesteps,andsorteverystepbasingtheirowntechnologyprinciples.Thewholesystemincludesthreelargekinds:purificationoftheproteins,analysisoftheprotein-proteininteractionsandproteinexpressiontechnologies.Andeverytechnologyincludesinferiorkinds.Thisclassifysystemhasgoodarrangementandiseasytounderstand.Afterreferringlotsofsimilarbioinformaticsdatabasessystem,weusethedesigncombinationofLinuxapacheMySQLandthencompletethedesignofadatabaseofprotein-proteininteractionsstudymethods.Thisdatabasewillmeetthestudiers’needstoprovidethemaflatroofofprovidingconvenientreferences,italsoprovidesmuchdependabledatainformationtomakethestudiestodomoreprofoundstudies,andgreatlyconvenientthemtomakeothercomparingstudies.Keywords:Protein-Proteininteraction,studymethods,databasesystemIII□_____□“√”111.1(HGP)(Functionalgenomics)mRNADNAproteomeproteingenome,19952080[1]HumanProteinIndex901996APAF(AustraliaProteomeAnalysisFacility)20014(HumanProteomeOrganizationHPO)(HumanProteomeProjectHPP)[2]-----221DNA-[3]1.2bioinformatics80Humangenomeproject1)2)SNP3)4)35)6)7)8)9)10)PSDSWISS-PROTPIRMIPS15DIPMedlineDNARNARNADNABINDPROTEOMEPRONETHelicobacterpylori1400PIMDIPDIP[4]DIP1999UCLADavidElsenbergDIPSQL4DIP1)1SWISSPROTPIRGenBank232)1233)1MEDLINE2320DIP1GenBankPIRSWISS-PROT2319998DIP1089126920026DIP180002100020042DIP801DIPSWISSPROTGenBankPIREcocyc,Flynet,YPD1.3WebWeb5Nature20025Stein[5]WebWeb(WebLab)EMBOSSBleasbyHalfdayontheWebsavesyouhalfmonthinthelab[5]WebWebWeb/B/S[6]1WebWebWebWebWebHTMLASCIIWebHTMLHTMLHTTP(HyperTextTransferProtoco1)6beWtneilCbeWrevreStenartnI/tenretnIlmth.xxx/revresbew//:ptthlmth.xxx1.1WebWeb[7]Web1.2CG1(CommonGatewayInterface)API(ApplicationProgramInterface)WebHTMLHTMLWebWebWebWebServerCGIAPI1.2WebWebApachePHPMySQLAPIMySQLPHPAPI1.47(1)(2)LinuxMySQL(3)1.5LinuxMySQLPHPAPI822.1,,,Fields,HIS3HIS3,HIS3HIS3,LacZ,(Gal4),,PCRPCRDNARNAPCRPCRPCRPCRPCRPCRRT-PCRPCRTailPCR9SDS-PAGEIEFMALDI-MS,BIAcore,BIAcoreBIAcoreBIAcore:RAMcCM-5-TSHRAMcTSH-TSH10[8-35]2.2[9](1)(2)(3)2.1112.1(Extraction)1(SolutionproteinExtraction[12])2(MenbraneproteinExtraction)(RoughFractionation)1(Saltout)2(Sedimentation)34(Dialyzation)5(Centrifugation)(Purification)1(Ultrafiltration)2(Gelfiltration)3(Affinitychromatography)4(Chromatofocusing)5(Immunoprecipitation)6(Ultracentrifugation)7(Ionexchangechromatography)8(Crystallology)(Concentration)1(Freezedryness)2(Vacuumdryness)3(Centrifugalvacuumevaporator)4(Crystallology)2.2PCR122.2(Electrophoresis)1(SDS-PAGE)2IEF/SDS-PAGE(2DIEF/SDS-PAGE)3(Capillaryelectrophoresis)(MS)1-(PLC-MS/MS)2(ESI-MS)3(MALDI-TOF-MS)4(MS/MS)(Photonics)1X(X-RayDiffractionXRD)2(NuclearMagneticResonanceNMR)3Fred4Biocore5SPR(MolecularBiology)1(Yeasttwo_hybrid)2(Three_bindinghybrid)3PCR4(Immunoprecipitation)(Highthroughput)1(Biochip)(Bioinformatics)1(Bioinformaticssoftware)2(WebDatabase)1333.1Linux+MySQL+Apache[36,37]LinuxMySQLSQLWindowsNTLinuxGPLMySQLApacheWebPHPLinux2.6.91.667MySQL3.23.58PHP4.3.93httpd2.0.5233.2LinuxLinuxLinuxUnix1991105LinusTorvalsIntelx86CPUIntelUnix[36-42]MicrosoftWindowsLinux[43]1(OSI142()Windows3LinuxWindowsORACLE8.1.6LINUXWIN2000SERVER35%4LinuxGUIWindows5LinuxLinux6LinuxLinuxWindows7LinuxWindowsLinuxLinuxLinuxLinuxLinuxLinux10.02.6.91.6673.3MySQL3.3.1MySQLMySQLMySQLT.c.XSQLMySQL/15mysqldMySQL[44]LinuxSQLmSQLPostgreSQLMySQLMySQLMySQLmSQLMySQLMySQLmSQLSQL1)MySQLmSQL2)MySQLmSQLmSQL3)MySQL4)MySQLVARCHAR5)MySQL6)MySQL7)MySQL8)mSQLGROUPBYPostgreSQLPostgreSQLANSISQLODBCPostgreSQLMySQLPostgreSQLMySQLWindowsLinuxMySQLMySQL3.23.583.3.2MySQLMySQL[45]mysqldump16mysqlimportmysqladminwMySQLMySQLMySQLMySQLSQLMySQLMySQLMySQL[46]1mysqlSQLSQLcursesS-LangTcl/TkXWebmysql2SQLSQLCSQLmysqlSQLmysql--forcemysqlmysql-[46]17MySQLWebMySQLWebMySQLWebWebMySQLWebWebMySQLWebWebMySQLMySQL1WebMySQLWebMySQL2WebMySQL3WebMySQL4WebMySQLMySQL3.3.3PHPMySQLPHPAPIPHPWebPHPWebWebLinuxPHPApacheApacheCGI[47]PHPHTMLPHPWebHTMLPHPPHPHTMLPHPPHP18PHPMySQL[46]MySQLPHP[](1)MySQL?php$link=mysql_connect(pit-viper,paulsecret)ordie(Couldnotconnect);print(Connectedsuccessfully);mysql_close($link)?mysql_connect(pit-viper,paulsecret)M