Tutorial生物信息学英文版,生物信息学,超强烈推

BiopythonTutorialandCookbookJeChang,BradChapman,IddoFriedbergLastUpdate{24October01Contents1Introduction31.1WhatisBiopython?.........................................31.1.1WhatcanIndinthebiopythonpackage.........................31.2ObtainingBiopython.........................................41.3Installation..............................................41.3.1InstallingfromsourceonUNIX...............................41.3.2InstallingfromsourceonWindows.............................51.3.3InstallingusingRPMs....................................61.3.4InstallingwithaWindowsInstaller.............................61.3.5InstallingonMacintosh...................................61.4Makingsureitworked........................................71.5FAQ..................................................72QuickStart{WhatcanyoudowithBiopython?92.1GeneraloverviewofwhatBiopythonprovides...........................92.2Workingwithsequences.......................................92.3Ausageexample...........................................132.4Parsingbiologicalleformats....................................132.4.1Generalparserdesign....................................132.4.2Writingyourownconsumer.................................142.4.3Makingiteasier.......................................162.4.4FASTAlesasDictionaries.................................172.4.5Iloveparsing{pleasedon'tstoptalkingaboutit!....................182.5Connectingwithbiologicaldatabases................................192.6Whattodonext...........................................203Cookbook{Coolthingstodowithit213.1BLAST................................................213.1.1RunningBLASTovertheinternet.............................213.1.2ParsingtheoutputfromthelefullofBLASTruns..............................273.1.7Findingabadrecordsomewhereinahugele......................283.1.8DealingwithPSIBlast....................................293.2SWISS-PROT.............................................293.2.1RetrievingaSWISS-PROTrecord.............................293.3PubMed................................................313.3.1SendingaquerytoPubMed.................................313.3.2RetrievingaPubMedrecord................................313.4GenBank...............................................3213.4.1RetrievingGenBankentriesfromNCBI..........................323.4.2ParsingGenBankrecords..................................333.4.3MakingyourveryownGenBankdatabase.........................343.5Dealingwithalignments.......................................343.5.1Clustalw............................................353.5.2Calculatingsummaryinformation.............................363.5.3Calculatingaquickconsensussequence..........................363.5.4PositionSpecicScoreMatrices...............................373.5.5InformationContent.....................................383.5.6TranslatingbetweenAlignmentformats..........................393.6SubstitutionMatrices........................................403.6.1Usingcommonsubstitutionmatrices............................403.6.2Creatingyourownsubstitutionmatrixfromanalignment................403.7MoreAdvancedSequenceClasses{SequenceIDsandFeatures.................413.7.1SequenceidsandDescriptions{dealingwithSeqRecords................423.7.2FeaturesandAnnotations{SeqFeatures..........................433.8Classication.............................................463.9BioCorba...............................................463.10Miscellaneous.............................................463.10.1TranslatingaDNAsequencetoProtein..........................464Advanced474.1SequenceClass............................................474.2RegressionTestingFramework...................................474.2.1WritingaRegressionTest..................................474.3ParserDesign.............................................484.3.1DesignOverview.......................................484.3.2Events.............................................484.3.3'noevent'EVENT......................................484.3.4Scanners............................................484.3.5Consumers..........................................494.3.6BLAST............................................494.3.7Enzyme............................................504.3.8Fasta.............................................514.3.9Medline............................................514.3.10Prosite.............................................524.3.11SWISS-PROT........................................524.4SubstitutionMatrices........................................534.4.1SubsMat............................................534.4.2FreqTable...........................................565Wheretogofromhere{contributingtoBiopython575.1Maintainingadistributionforaplatform............................