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BIOINFORMATICS ALGORITHMS Techniques and Applications Editedby IonI.Ma˘ndoiuandAlexanderZelikovsky AJOHNWILEY&SONS,INC.,PUBLICATION BIOINFORMATICS ALGORITHMS BIOINFORMATICS ALGORITHMS Techniques and Applications Editedby IonI.Ma˘ndoiuandAlexanderZelikovsky AJOHNWILEY&SONS,INC.,PUBLICATION Copyright©2008byJohnWiley&Sons,Inc.Allrightsreserved. PublishedbyJohnWiley&Sons,Inc.,Hoboken,NewJersey PublishedsimultaneouslyinCanada Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedinanyformor byanymeans,electronic,mechanical,photocopying,recording,scanningorotherwise,exceptas permittedunderSections107or108ofthe1976UnitedStatesCopyrightAct,withouteithertheprior writtenpermissionofthePublisher,orauthorizationthroughpaymentoftheappropriateper-copyfeeto theCopyrightClearanceCenter,Inc.,222RosewoodDrive,Danvers,MA01923,978-750-8400,fax 978-646-8600,oronthewebatwww.copyright.com.RequeststothePublisherforpermissionshouldbe addressedtothePermissionsDepartment,JohnWiley&Sons,Inc.,111RiverStreet,Hoboken,NJ 07030,(201)-748-6011,fax(201)-748-6008. LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthorhaveusedtheirbesteffortsin preparingthisbook,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyor completenessofthecontentsofthisbookandspecificallydisclaimanyimpliedwarrantiesof merchantabilityorfitnessforaparticularpurpose.Nowarrantymaybecreatedorextendedbysales representativesorwrittensalesmaterials.Theadviceandstrategiescontainedhereinmaynotbesuitable foryoursituation.Youshouldconsultwithaprofessionalwhereappropriate.Neitherthepublishernor authorshallbeliableforanylossofprofitoranyothercommericaldamages,includingbutnotlimitedto special,incidental,consequential,orotherdamages. ForgeneralinformationonourotherproductsandservicespleasecontactourCustomerCareDepartment withintheU.S.at877-762-2974,outsidetheU.S.at317-572-3993orfax317-572-4002. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprint, however,maynotavailableinelectronicformat. LibraryofCongressCataloging-in-PublicationData: Bioinformaticsalgorithms:techniquesandapplications/editedbyIonI. MandoiuandAlexanderZelikovsky. p.cm. ISBN978-0-470-09773-1(cloth) 1. Bioinformatics.2. Algorithms. I.Mandoiu,Ion.II.Zelikovsky, Alexander. QH324.2B5472 2008 572.80285–dc22 2007034307 PrintedintheUnitedStatesofAmerica 10 9 8 7 6 5 4 3 2 1 CONTENTS Preface ix Contributors xi 1 EducatingBiologistsinthe21stCentury:BioinformaticsScientists versusBioinformaticsTechnicians 1 PavelPevzner PARTI TECHNIQUES 7 2 DynamicProgrammingAlgorithmsforBiologicalSequence andStructureComparison 9 YuzhenYeandHaixuTang 3 GraphTheoreticalApproachestoDelineateDynamics ofBiologicalProcesses 29 TeresaM.PrzytyckaandElenaZotenko 4 AdvancesinHiddenMarkovModelsforSequenceAnnotation 55 BronˇaBrejova´,DanielG.Brown,andToma´sˇVinarˇ 5 Sorting-andFFT-BasedTechniquesintheDiscoveryofBiopatterns 93 SudhaBalla,SanguthevarRajasekaran,andJaimeDavila v vi CONTENTS 6 ASurveyofSeedingforSequenceAlignment 117 DanielG.Brown 7 TheComparisonofPhylogeneticNetworks:Algorithms andComplexity 143 PaolaBonizzoni,GianlucaDellaVedova,RiccardoDondi,and GiancarloMauri PARTII GENOMEANDSEQUENCEANALYSIS 175 8 FormalModelsofGeneClusters 177 AnneBergeron,CedricChauve,andYannickGingras 9 IntegerLinearProgrammingTechniquesforDiscovering ApproximateGeneClusters 203 SvenRahmannandGunnarW.Klau 10 EfficientCombinatorialAlgorithmsforDNA SequenceProcessing 223 BhaskarDasGuptaandMing-YangKao 11 AlgorithmsforMultiplexPCRPrimerSetSelectionwith AmplificationLengthConstraints 241 K.M.Konwar,I.I.Ma˘ndoiu,A.C.Russell,andA.A.Shvartsman 12 RecentDevelopmentsinAlignmentandMotifFinding forSequencesandNetworks 259 Sing-HoiSze PARTIII MICROARRAYDESIGNANDDATAANALYSIS 277 13 AlgorithmsforOligonucleotideMicroarrayLayout 279 Se´rgioA.DeCarvalhoJr.andSvenRahmann 14 ClassificationAccuracyBasedMicroarrayMissingValue Imputation 303 YiShi,ZhipengCai,andGuohuiLin 15 Meta-AnalysisofMicroarrayData 329 SaumyadiptaPyne,SteveSkiena,andBruceFutcher CONTENTS vii PARTIV GENETICVARIATIONANALYSIS 353 16 PhasingGenotypesUsingaHiddenMarkovModel 355 P.Rastas,M.Koivisto,H.Mannila,andE.Ukkonen 17 AnalyticalandAlgorithmicMethodsforHaplotype FrequencyInference:WhatDoTheyTellUs? 373 StevenHechtOrzack,DanielGusfield,LakshmanSubrahmanyan, LaurentEssioux,andSebastienLissarrague 18 OptimizationMethodsforGenotypeDataAnalysis inEpidemiologicalStudies 395 DumitruBrinza,JingwuHe,andAlexanderZelikovsky PARTV STRUCTURALANDSYSTEMSBIOLOGY 417 19 TopologicalIndicesinCombinatorialChemistry 419 SergeyBereg 20 EfficientAlgorithmsforStructuralRecallinDatabases 439 HaoWang,PatraVolarath,andRobertW.Harrison 21 ComputationalApproachestoPredictProtein–Protein andDomain–DomainInteractions 465 RajaJothiandTeresaM.Przytycka Index 493

Bioinformatics algorithms : techniques and applications PDF

518 Pages·2008·5.74 MB·English

by Ion Măndoiu, Alexander Zelikovsky

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Author:	Ion Măndoiu; Alexander Zelikovsky
Publication Year:	2008
ISBN:	470253444
Pages:	518
Language:	English
File Size:	5.74
Format:	PDF
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