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1、http://www.paper.edu.cnImprovedTabooSearchAlgorithmforDesigningDNAWordsKaiZhang,JinXu,XiutangGeng,JianhuaXiao,andLinqiangPan?KeyLaboratoryofImageProcessingandIntelligentControlDepartmentofControlScienceandEngineeringHuazhongUniversityofScienceandTechnologyWuhan430074,Chinazhangkaicn@sin
2、a.com,jxu@mail.hust.edu.cngxt1028@163.com,jhxiao2008@163.com,lqpan@mail.hust.edu.cnAbstract.ThedesignofDNAsequencesisoneofthemostpracticalandimportantresearchtopicsinDNAcomputing.Weadopttaboosearchalgorithmandimprovedthemethodforthesystematicdesignofequal-lengthDNAsequences,whichcouldsa
3、tisfycertaincombinatorialandthermodynamicconstraints.Usingtaboosearchalgorithm,ourmethodcanavoidtrappingintolocaloptimizationandcanˉndgreatestDNAsequencessetswhichsatisfyrequiredconstraints.Keywords:DNAComputing;TabooSearchAlgorithm;DNASequencesDesign1IntroductionSinceAdleman[1]ˉrstlypr
4、esentedtheexperimentbyusingmolecularbiologytosolvea7-vertexinstanceofHamiltonianPathProblemin1994,DNAcomputingshowsgreatpotentialtosolvepainstakingproblemssuchastheNP-completeproblems.DNAsequencesdesignisoneofthemostpracticalandimportantresearchtopicsinDNAcomputing.Inordertoobtainsucces
5、sfulresultsofbiologicalexperiments,wemustdesigne?ectiveDNAsequencesfortargetcomputationalproblem.TherehasbeenagreatdealofpreviousworkindesigningDNAsequences[2][3][4][5].Inparticular,Frutos[6][7]etal.proposedthetemplatemethodforDNAworddesign.Feldkamp[8]demonstratedaDNAsequencecompileralg
6、orithmfordesigningDNAsequences.Reaton[9][10][11]presentedageneticalgorithmforgeneratingDNAstrands.However,theobviousdisadvantageofthecurrentDNAgeneratoralgorithmisthepossibilityofbeingtrappedinlocaloptimizationwhichmaybefarfromtheglobaloptimalsolution.Taboosearchisageneraltechniquepropo
7、sedbyGlover[12][13]forobtainingapproximatesolutionstocombi-natorialoptimizationproblems.Taboosearchavoidsbeingtrappedintolocalminimumbyallowingthetemporalacceptanceofworsesolution.Andithasbeensuccessfullyappliedtoawiderangeofcombinatorialoptimizationproblemssuchasjobshopschedul
