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1、TutorialonDNAComputingandGraphTransformationTeroHarju1,IonPetre2,andGrzegorzRozenberg31DepartmentofMathematics,UniversityofTurku,FIN-20014Turku,Finland.email:harju@utu.fi2DepartmentofComputerScience,˚AboAcademiUniversity,FIN-20520Turku,Finland.email:ion.petre@abo.fi3LeidenInstituteforAdva
2、ncedComputerScience,LeidenUniversity,NielsBohrweg1,2333CALeiden,theNetherlands,andDepartmentofComputerScience,UniversityofColoradoatBoulder,Boulder,Co80309-0347,USA.email:rozenber@liacs.nlDNAcomputing,ormoregenerallyMolecularcomputingisanexcitingresearchareaattheintersectionofmathematics,
3、computerscienceandmolecularbiology.ResearchinDNAcomputingcanberoughlydividedintwostreams:DNAcom-putinginvitroandinvivo.Theformerisconcernedwithbuilding(specialized)DNA-basedcomputersintesttubes,whilethelatterisconcernedwithimple-mentingsomecomputationalcomponentsinlivingcells,aswellaswith
4、studyingthecomputationalprocessestakingplaceinthelivingcells.Inthistutorial,weshalldiscussthecomputationalnatureofaveryintri-cateDNAprocessingtakingplaceinsinglecellorganismscalledciliates,intheprocessofgeneassembly.Weshalldiscusstheroleofgraphtransformationsinmodellingandstudyinggeneasse
5、mblyprocess.Inparticular,wedemonstratethatgraphtransformationsprovidetherightlevelofabstraction,andusefultech-nicaltoolsforstudyinggeneassembly.Ontheotherhand,thegeneassemblyprocessinspiresanewcomputingparadigm;computingbyfoldingandrecom-bination,whichinducesnovelquestionsandchallengesfor
6、researchongraphtransformation.1NucleardualismofciliatesCiliatesareanancientgroupofsinglecellorganismsthathaveauniquenu-cleardualism:theyhavetwokindsofnuclei,thegermlinemicronucleusandthesomaticmacronucleus.Thegeneticinformationisencodedinverydifferentwaysinthetwotypesofnuclei.Inthemicronuc
7、leus,thegenesareplacedinlongcontinuousDNAmoleculesinterruptedbynoncodingspacerDNA.Inthemacronucleus,theDNAispresentinshort,gene-sizemolecules.Duringsexualreproductionciliatesconvertthemicronucleargenomeintothemacronucleargenome,eliminatingallthenoncodingDNA,andtrans
