beginning perl for bioinformatics - james tisdall

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1、IT-SCBeginningPerlforBioinformaticsJamesTisdallPublisher:O'ReillyFirstEditionOctober2001ISBN:0-596-00080-4,384pagesThisbookshowsbiologistswithlittleornoprogrammingexperiencehowtousePerl,theideallanguageforbiologicaldataanalysis.Eachchapterfocusesonsolvingparticularproblemsorclas

2、sofproblems,soyou'llfinishthebookwithasolidunderstandingofPerlbasics,acollectionofprogramsforsuchtasksasparsingBLASTandGenBank,andtheskillstotacklemoreadvancedbioinformaticsprogramming.$IT-SCIT-SC2PrefaceWhatIsBioinformatics?AboutThisBookWhoThisBookIsForWhyShouldILearntoProgram?

3、StructureofThisBookConventionsUsedinThisBookCommentsandQuestionsAcknowledgments1.BiologyandComputerScience1.1TheOrganizationofDNA1.2TheOrganizationofProteins1.3InSilico1.4LimitstoComputation2.GettingStartedwithPerl2.1ALowandLongLearningCurve2.2Perl'sBenefits2.3InstallingPerlonYo

4、urComputer2.4HowtoRunPerlPrograms2.5TextEditors2.6FindingHelp3.TheArtofProgramming3.1IndividualApproachestoProgramming3.2Edit—Run—Revise(andSave)3.3AnEnvironmentofPrograms3.4ProgrammingStrategies3.5TheProgrammingProcess4.SequencesandStrings4.1RepresentingSequenceData4.2AProgramt

5、oStoreaDNASequence4.3ConcatenatingDNAFragments4.4Transcription:DNAtoRNA4.5UsingthePerlDocumentation4.6CalculatingtheReverseComplementinPerl4.7Proteins,Files,andArrays4.8ReadingProteinsinFiles4.9Arrays4.10ScalarandListContext4.11Exercises5.MotifsandLoops5.1FlowControl5.2CodeLayou

6、t5.3FindingMotifs5.4CountingNucleotides5.5ExplodingStringsintoArrays5.6OperatingonStrings5.7WritingtoFilesIT-SC15.8Exercises6.SubroutinesandBugs6.1Subroutines6.2ScopingandSubroutines6.3Command-LineArgumentsandArrays6.4PassingDatatoSubroutines6.5ModulesandLibrariesofSubroutines6.

7、6FixingBugsinYourCode6.7Exercises7.MutationsandRandomization7.1RandomNumberGenerators7.2AProgramUsingRandomization7.3AProgramtoSimulateDNAMutation7.4GeneratingRandomDNA7.5AnalyzingDNA7.6Exercises8.TheGeneticCode8.1Hashes8.2DataStructuresandAlgorithmsforBiology8.3TheGeneticCode8.

8、4TranslatingDNAintoProteins8.5ReadingDNAfromFil