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1、PermutedSubstringMatching,withApplicationstoComputationalBiologyByHoumanAlborziAnAbstractofAThesisSubmittedtoMichiganStateUniversityinpartialful llmentoftherequirementsforthedegreeofMasterofScienceDepartmentofComputerScience1997ProfessorEricTorngPermutedSubstringMatching,withApplications
2、toComputationalBiologyByHoumanAlborziAThesisSubmittedtoMichiganStateUniversityinpartialful llmentoftherequirementsforthedegreeofMasterofScienceDepartmentofComputerScience1997AbstractPermutedSubstringMatching,withApplicationstoComputationalBiologyByHoumanAlborziWeproposeanewinexpensivetec
3、hniqueto ndtheDNAsequenceofgenes.Thetechniqueisbasedupon ndingthelocationofafragmentofagenomeusingtherestrictionmapofthegenomeandtherestrictionpatternofthefragment.Astheremaybemorethanonelocationonthegenomematchingtherestrictionpatternofthefragment,weinvestigatethee ectivenessofourtechni
4、quebasedonhowpreciselyitcandeterminethelocationofthefragment.Weshowthatthesizeoftherestrictionpatternofthefragmentistheprimaryparameterthata ectsthee ectivenessofourtechnique.Wehavealsodesignedandimplementedfastalgorithmsforlocatingthefragment.Dedicatedtotheadvancementoffrontiers.iiiAckn
5、owledgmentsIwouldliketothankDr.EricTorng,myacademicadvisorwhowasalwaystryingtoputorderinmychaoticwork.Withouthispatienceandsupport,completingthisthesiswouldnothavebeenpossible.Dr.SaktiPramanikandDr.JamesColewerealwayseagertodiscussmywork.Iamgratefulfortheirhelpandtimeallottedtothisprojec
6、t.Mytechnicalthankstothesta ofthecomputersciencedepartmentcomputingserviceswhoprovidedthesupportandmaintenanceneededforthisproject.Finally,Iwouldliketothankthefaculty,sta ,andstudentsofthecomputersciencedepartmentwithwhomIworked.Theywerealwaysencouraging.ivTableofContentsLISTOFTABLESviLI
7、STOFFIGURESvii1Introduction11.1Genome,Genes,andDNA..........................11.2RestrictionEnzymes.............................31.3FormalDe nitions..............................51.4ProblemStatement..............................61.5BackgroundonSearching....................
