An Efficient Rank Based Approach for Closest String and Closest Substring 英文参考文献.docVIP

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An Efficient Rank Based Approach for Closest String and Closest Substring 英文参考文献.doc

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An Efficient Rank Based Approach for Closest String and Closest Substring 英文参考文献

AnEfficientRankBasedApproachforClosestStringand ClosestSubstring LiviuP.Dinu*.,RaduIonescu. FacultyofMathematicsandComputerScience,UniversityofBucharest,Bucharest,Romania Abstract ThispaperaimstopresentanewgeneticapproachthatusesrankdistanceforsolvingtwoknownNP-hardproblems,andto compare rank distance with other distance measures for strings. The two NP-hard problems we are trying to solve are closeststringandclosestsubstring.Foreachproblemwebuildageneticalgorithmandwedescribethegeneticoperations involved.Bothgeneticalgorithms useafitnessfunctionbasedonrankdistance.Wecompareouralgorithms withother geneticalgorithmsthatusedifferentdistancemeasures,suchasHammingdistanceorLevenshteindistance,onrealDNA sequences.Ourexperimentsshowthatthegeneticalgorithmsbasedonrankdistancehavethebestresults. Citation: Dinu LP, Ionescu R (2012) An Efficient Rank Based Approach for Closest String and Closest Substring. PLoS ONE 7(6): e37576. doi:10.1371/ journal.pone.0037576 Editor:ChuhsingKateHsiao,NationalTaiwanUniversity,Taiwan ReceivedDecember10,2011;AcceptedApril24,2012;PublishedJune4,2012 Copyright: ? 2012 Dinu, Ionescu. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Thisresearchwasconductedwithoutanyfunds.TheauthorssupportedthisworkfromtheirsalaryasresearchersattheUniversityofBucharest.The fundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:ldinu@fmi.unibuc.ro .Theseauthorscontributedequallytothiswork. Introduction foraseriesofindividualcharactersorcharacterspatternsthatare inthesameorderinthesequences.Algorithmically,thestandard pairwise alignment method is based on dynamic programming; themethodcompareseverypairofcharactersofthetwosequences and generates an align