Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins

646 Pages·2020·21.016 MB·English

by  Andreas D. Baxevanis (Editor), Gary D. Bader (Editor), David S. Wishart (Editor)

Bioinformatics

Bioinformatics
Edited by
Andreas D. Baxevanis, Gary D. Bader, and David S. Wishart
FourthEdition
Thisfourtheditionfirstpublished2020
©2020JohnWiley&Sons,Inc.
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LibraryofCongressCataloging-in-PublicationData
Names:Baxevanis,AndreasD.,editor.|Bader,GaryD.,editor.|Wishart,
DavidS.,editor.
Title:Bioinformatics/editedbyAndreasD.Baxevanis,GaryD.Bader,DavidS.
Wishart.
Othertitles:Bioinformatics(Baxevanis)
Description:Fourthedition.|Hoboken,NJ:Wiley,2020.|Includes
bibliographicalreferencesandindex.
Identifiers:LCCN2019030489(print)|ISBN9781119335580(cloth)|ISBN
9781119335962(adobepdf)|ISBN9781119335955(epub)
Subjects:MESH:ComputationalBiology–methods|SequenceAnalysis–methods
|BaseSequence|Databases,NucleicAcid|Databases,Protein
Classification:LCCQH324.2(print)|LCCQH324.2(ebook)|NLMQU
550.5.S4|DDC570.285–dc23
LCrecordavailableathttps://lccn.loc.gov/2019030489
LCebookrecordavailableathttps://lccn.loc.gov/2019030490
CoverDesign:Wiley
CoverImages:©DavidWishart,background©Suebsiri/GettyImages
Setin9.5/12.5ptSTIXTwoTextbySPiGlobal,Chennai,India
10 9 8 7 6 5 4 3 2 1
v
Contents
Foreword vii
Preface ix
Contributors xi
AbouttheCompanionWebsite xvii
1 BiologicalSequenceDatabases 1
AndreasD.Baxevanis
2 InformationRetrievalfromBiologicalDatabases 19
AndreasD.Baxevanis
3 AssessingPairwiseSequenceSimilarity:BLASTandFASTA 45
AndreasD.Baxevanis
4 GenomeBrowsers 79
TyraG.Wolfsberg
5 GenomeAnnotation 117
DavidS.Wishart
6 PredictiveMethodsUsingRNASequences 155
MichaelF.Sloma,MichaelZuker,andDavidH.Mathews
7 PredictiveMethodsUsingProteinSequences 185
JonasReeb,TatyanaGoldberg,YanayOfran,andBurkhardRost
8 MultipleSequenceAlignments 227
FabianSievers,GeoffreyJ.Barton,andDesmondG.Higgins
9 MolecularEvolutionandPhylogeneticAnalysis 251
EmmaJ.GriffithsandFionaS.L.Brinkman
10 ExpressionAnalysis 279
MariekeL.Kuijjer,JosephN.Paulson,andJohnQuackenbush
11 ProteomicsandProteinIdentificationbyMassSpectrometry 315
SadhnaPhanseandAndrewEmili
12 ProteinStructurePredictionandAnalysis 363
DavidS.Wishart
13 BiologicalNetworksandPathways 399
GaryD.Bader
vi Contents
14 Metabolomics 437
DavidS.Wishart
15 PopulationGenetics 481
LynnB.JordeandW.ScottWatkins
16 MetagenomicsandMicrobialCommunityAnalysis 505
RobertG.Beiko
17 TranslationalBioinformatics 537
SeanD.MooneyandStephenJ.Mooney
18 StatisticalMethodsforBiologists 555
HunterN.B.Moseley
Appendices 583
Glossary 591
Index 609
vii
Foreword
AsIreviewthematerialpresentedinthefourtheditionofBioinformaticsIammovedintwo
ways,relatedtoboththepastandthefuture.
Lookingtothepast,Iammovedbytheamazingevolutionthathasoccurredinourfield
sincethefirsteditionofthisbookappearedin1998.Twenty-oneyearsisalong,longtimein
anyscientificfield,butespeciallysointheagilefieldofbioinformatics.Tousethewell-trodden
metaphorofthe“biologymoonshot,”thelaunchpadatthebeginningofthetwenty-firstcen-
turywasthedeterminationofthehumangenome.Discoveryisnottherightwordforwhat
transpired–weknewitwasthereandwhatwasneeded.Synergyisperhapsabetterword;
synergyoftechnologicaldevelopment,experiment,computation,andpolicy.Atrulycollabo-
rativeefforttocontinuouslyshare,inareusableway,thecollectiveeffortsofmanyscientists.
Bioinformaticswasbornfromthissynergyandhascontinuedtogrowandflourishbasedon
theseprinciples.
Thatgrowthisreflectedinboththescopeanddepthofwhatiscoveredinthesepages.These
attributesareareflectionoftheincreasedcomplexityofthebiologicalsystemsthatwestudy
(moving from “simple” model organisms to the human condition) and the scales at which
those studies take place. As a community we have professed multiscale modeling without
muchtoshowforit,butitwouldseemtobefinallyhere.Wenowhavetheabilitytoconnectthe
dotsfrommolecularinteractions,throughthepathwaystowhichthosemoleculesbelongto
thecellstheyaffect,totheinteractionsbetweenthosecellsthroughtotheeffectstheyhaveon
individualswithinapopulation.Toolsandmethodologiesthatwerenovelinearliereditions
ofthisbookarenowroutineorobsolete,andnewer,faster,andmoreaccurateproceduresare
nowwithus.Thiswillcontinue,andassuchthisbookprovidesavaluablesnapshotofthe
scopeanddepthofthefieldasitexiststoday.
Lookingtothefuture,thisbookprovidesafoundationforwhatistocome.Formethisis
a field more aptly referred to (and perhaps a new subtitle for the next edition) as Biomedi-
calDataScience.SittingasIdonow,asDeanofaSchoolofDataSciencewhichcollaborates
openlyacrossalldisciplines,Iseerapidchangeakintowhathappenedtobirthbioinformat-
ics20ormoreyearsago.Itwillnottake20yearsforotherdisciplinestocatchup;Ipredictit
willtake2!Theaccomplishmentsoutlinedinthisbookcanhelpdefinewhatotherdisciplines
willaccomplishwiththeirowndataintheyearstocome.Statisticalmethods,cloudcomput-
ing,dataanalytics,notablydeeplearning,themanagementoflargedata,visualization,ethics
policy,andthelawsurroundingdataaregeneric.Bioinformaticshassomuchtooffer,yetit
willalsobeinfluencedbyotherfieldsinawaythathasnothappenedbefore.Forty-fiveyears
inacademiatellsmethatthereisnothingtocompareacrosscampusestowhatishappening
today.Thisisbothanopportunityandathreat.Theeditorsandauthorsofthiseditionshould
becomplimentedforsettingthestageforwhatistocome.
PhilipE.Bourne,UniversityofVirginia