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基于多核和众核平台的并行DNA序列比对算法.docx

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基于多核和众核平台的并行DNA序列比对算法 Title:ParallelDNASequenceAlignmentAlgorithmsforMulti-coreandMany-corePlatforms Abstract: WiththerapidadvancementsinDNAsequencingtechnology,theamountofDNAsequencedatageneratedhasincreasedexponentially.DNAsequencealignment,whichinvolvescomparingandfindingsimilaritiesinDNAsequences,formsacrucialstepinvariousbioinformaticsapplications.However,duetothegrowingsizeofDNAdatasets,traditionalsequentialalignmentalgorithmscannotefficientlyhandlethecomputationalburden.Toovercomethischallenge,parallelDNAsequencealignmentalgorithmshavebeendevelopedtoleveragethecomputationalpowerofferedbymulti-coreandmany-coreplatforms.ThispaperaimstoexploreanddiscussvariousapproachesandtechniquesemployedindesigningparallelDNAsequencealignmentalgorithmsforsuchplatforms. 1.Introduction: 1.1Background: DNAsequencinghasbecomeincreasinglyaccessibleandaffordable,leadingtothegenerationofmassiveamountsofDNAsequencedata.Efficientanalysisandalignmentofthisdataiscrucialforvariousbiologicalandmedicalresearchapplications. 1.2ProblemStatement: TraditionalsequentialDNAsequencealignmentalgorithmsareunabletohandlethecomputationalchallengesposedbylarge-scaleDNAdatasets.Asaresult,parallelalgorithmshaveemergedasapromisingsolutiontoacceleratethealignmentprocessonmulti-coreandmany-coreplatforms. 1.3Objective: TheobjectiveofthispaperistodiscussthedesignandimplementationconsiderationsofparallelDNAsequencealignmentalgorithmsonmulti-coreandmany-coreplatforms,aswellaspresentanoverviewofexistingapproachesandtechniques. 2.ParallelComputing: 2.1Multi-coreandMany-corePlatforms: Thissectionprovidesanoverviewofmulti-coreandmany-coreplatforms,highlightingtheircharacteristicsandadvantagesintermsofparallelcomputingperformance.Italsodiscussestheimportanceofloadbalancinganddatapartitioninginparallelalgorithms. 2.2ParallelProgrammingModels: Variousparallelprogrammingmodels,suchassharedmemoryandmessagepassing,arediscussedinthissection.Thechoiceofprogrammingmodeldependsontheplatform'sarchitectureandtherequirementsof