Bioinformatics for DNA Sequence Analysis

358 Pages·2009·6.9 MB·English

by  Kit J. Menlove

M M B TM
ETHODS IN OLECULAR IOLOGY
SeriesEditor
JohnM.Walker
SchoolofLifeSciences
UniversityofHertfordshire
Hatfield,Hertfordshire,AL109AB,UK
Forothertitlespublishedinthisseries,goto
www.springer.com/series/7651
M M B TM
ETHODS IN OLECULAR IOLOGY
Bioinformatics for DNA Sequence
Analysis
Edited by
David Posada
Departamento de Gene´tica, Bioqu´ımica e Inmunolog´ıa,
Facultad de Biolog´ıa, Universidad de Vigo,
Vigo, Spain
Editor
DavidPosada
DepartamentodeGene´tica
Bioqu´ımicaeInmunolog´ıa
FacultaddeBiolog´ıa
UniversidaddeVigo
Vigo
Spain
[email protected]
ISSN1064-3745 e-ISSN1940-6029
ISBN978-1-58829-910-9 e-ISBN978-1-59745-251-9
DOI10.1007/978-1-59745-251-9
LibraryofCongressControlNumber:2008941278
#HumanaPress,apartofSpringerScienceþBusinessMedia,LLC2009
Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewrittenpermissionofthe
publisher (Humana Press,c/o Springer ScienceþBusinessMedia, LLC, 233 Spring Street, New York, NY 10013,
USA),exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysis.Useinconnectionwithanyformof
informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology
nowknownorhereafterdevelopedisforbidden.
Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,eveniftheyarenotidentifiedas
such,isnottobetakenasanexpressionofopinionastowhetherornottheyaresubjecttoproprietaryrights.
Printedonacid-freepaper
springer.com
To Mo´nica and Lucas
Preface
Therecentaccumulationofinformationfromgenomes,includingtheirsequences,has
resultednotonlyinnewattemptstoansweroldquestionsandsolvelongstandingissues
inbiology,butalsointheformulationofnovelhypothesesthatarisepreciselyfromthis
wealth of data. The storage, processing, description, transmission, connection, and
analysis of these data has prompted bioinformatics to become one the most relevant
applied sciences for this new century, walking hand-in-hand with modern molecular
biologyandclearlyimpactingareaslikebiotechnologyandbiomedicine.
Bioinformatics skills have now become essential for many scientists working with
DNA sequences. With this idea in mind, this book aims to provide practical guidance
andtroubleshootingadviceforthecomputationalanalysisofDNAsequences,covering
a range of issues and methods that unveil the multitude of applications and relevance
that Bioinformatics has today. The analysis of protein sequences has been purposely
excludedtogainfocus.Individualbookchaptersareorientedtowardthedescriptionof
theuseofspecificbioinformaticstools,accompaniedbypracticalexamples,adiscussion
ontheinterpretationofresults,andspecificcommentsonstrengthsandlimitationsof
the methods and tools. In a sense, chapters could be seen as enriched task-oriented
manualsthatwilldirectthereaderincompletingspecificbioinformaticsanalyses.
The target audience for this book is biochemists, and molecular and evolutionary
biologiststhatwanttolearnhowtoanalyzeDNAsequencesinasimplebutmeaningful
fashion. Readers do not need a special background in statistics, mathematics, or
computer science, just a basic knowledge of molecular biology and genetics. All the
tools described in the book are free and all of them can be downloaded or accessed
throughtheweb.Mostchapterscouldbeusedforpracticaladvancedundergraduateor
graduate-levelcoursesinbioinformaticsandmolecularevolution.
The book could not start in another place than describing one of the most wide-
spreadbioinformaticstool:BLAST(BasicLocalAlignmentSearchTool).Indeed,one
of the first steps in the analysis of DNA sequences is their collection. Therefore,
Chapter 1 guides the reader through the recognition of similar sequences using
BLAST. Next, the use of OrthologID for understanding the nature of this similarity
is describedin Chapter2, followedbya Chapter3 aboutone of the mostimportant
stages in most bioinformatics pipelines, the alignment, which shows the basis and
the application of the program MAFFT. The next set of chapters is intimately related
tothestudyofmolecularevolution.Indeed,theDNAsequencesthatweseetodayare
theresultofthisprocess.InChapter4,SeqVisisusedtodetectcompositionalchanges
inDNAsequencesthroughtime,whileChapter5isfocusedontheselectionofmodels
of nucleotide substitution using jModelTest. Precisely the use of these models for
phylogenetic reconstruction is described in Chapter 6, which capitalizes upon the
estimationofmaximumlikelihoodphylogenetictreeswithPhyml.Indeed,theestima-
tion of phylogenies is often the first step in many evolutionary analyses. How to
combine multiple trees in a single supertree is the basis of Chapter 7, which explains
vii
viii Preface
theuseoftheprogramClann.Next,Chapters8and9arecenteredonthecharacter-
ization of two key evolutionary processes acting on DNA sequences. The use of the
server Datamonkey for the detection of selection is described in Chapter 8, while
Chapter9showsthenutsandboltsofthedetectionofrecombinationusingRDP3.
The study of codon usage, which has provided many important insights at the
genomicscale,isdecipheredinChapter10usingCodonExplorer,aninteractivedata
base, while Chapter 11 explains how differences in the genetic code can be detected
using GenDecoder. The next chapters are related to the annotation of genomes, an
essential requisite for many other analyses. In Chapter 12, we learn how to predict
genesusingGeneID,whileinChapter13theidentificationofregulatorymotifswith
A-Glamisdescribed.Chapter14thenexplainstheuseoftheUCSCgenomebrowser
and its applications, for example, to characterize a gene or to explore conserved
elements. The discovery of single nucleotide polymorphisms (SNPs) and simple
sequence repeats (SSRs) with bioinformatics tools SNPServer, dbSNP, and SSR Tax-
onomyTreeisthesubjectofChapter15,andChapter16highlightstheuseofCensor
andRepeatMaskerforthedetectionandcharacterizationoftransposableofsequences
ineukaryoticgenomes.Toendthebook,Chapter17explainshowtomakethemostof
DnaSPfortheanalysisofDNAsequencesinpopulations.
I am very grateful to all the authors, the fundamental piece, who have put a lot of
effort replying patiently to all my queries. Hopefully, the result has been a set of clear
andusefulchaptersthatwillbeofhelptootherscientists.Iwanttothankallofthemfor
sharing their time, wisdom and expertise. Finally, I want to thank John Walker, the
editoroftheseries,forhiscontinuousadvice.
Vigo,July2008 DavidPosada
Contents
Preface............................................................ vii
Contributors........................................................ xi
1. SimilaritySearchingUsingBLAST..................................... 1
KitJ.Menlove,MarkClement,andKeithA.Crandall
2. GeneOrthologyAssessmentwithOrthologID ............................ 23
MaryEgan,ErnestK.Lee,JoannaC.Chiu,GloriaCoruzzi,
andRobDeSalle
3. MultipleAlignmentofDNASequenceswithMAFFT ...................... 39
KazutakaKatoh,GeorgeAsimenos,andHiroyukiToh
4. SeqVis:AToolforDetectingCompositionalHeterogeneityAmongAligned
NucleotideSequences............................................... 65
LarsSommerJermiin,JoshuaWingKeiHo,KwokWaiLau,
andVivekJayaswal
5. SelectionofModelsofDNAEvolutionwithjMODELTEST ................... 93
DavidPosada
6. EstimatingMaximumLikelihoodPhylogenieswithPhyML.................. 113
Ste´phaneGuindon,Fre´de´ricDelsuc,Jean-Franc¸oisDufayard,
andOlivierGascuel
7. TreesfromTrees:ConstructionofPhylogeneticSupertreesUsingClann ....... 139
ChristopherJ.CreeveyandJamesO.McInerney
8. DetectingSignaturesofSelectionfromDNASequencesUsingDatamonkey..... 163
ArtF.Y.Poon,SimonD.W.Frost,andSergeiL.KosakovskyPond
9. RecombinationDetectionandAnalysisUsingRDP3....................... 185
DarrenP.Martin
10. CodonExplorer:AnInteractiveOnlineDatabasefortheAnalysis
ofCodonUsageandSequenceComposition............................. 207
JesseZaneveld,MicahHamady,NoboruSueoka,andRobKnight
11. GeneticCodePredictionforMetazoanMitochondriawithGenDecoder........ 233
FedericoAbascal,RafaelZardoya,andDavidPosada
12. ComputationalGeneAnnotationinNewGenomeAssembliesUsingGeneID ... 243
EnriqueBlancoandJosepF.Abril
13. PromoterAnalysis:GeneRegulatoryMotifIdentificationwithA-GLAM ....... 263
LeonardoMarin˜o-Ramı´rez,KannanTharakaraman,JohnL.Spouge,
andDavidLandsman
14. AnalysisofGenomicDNAwiththeUCSCGenomeBrowser ................ 277
JonathanPevsner
15. MiningforSNPsandSSRsUsingSNPServer,dbSNP
andSSRTaxonomyTree ............................................ 303
JacquelineBatleyandDavidEdwards
ix
x Contents
16. AnalysisofTransposableElementSequencesUsingCENSOR
andRepeatMasker.................................................. 323
AhsanHudaandI.KingJordan
17. DNASequencePolymorphismAnalysisUsingDnaSP...................... 337
JulioRozas
Index ............................................................. 351
Contributors
FEDERICOABASCAL (cid:129) DepartamentodeGene´tica,Bioquı´micaeInmunologı´a,Facultad
deBiologı´a,UniversidaddeVigo,Vigo,Spain
JOSEP F. ABRIL (cid:129) Departament de Gene`tica, Facultat de Biologia, Universitat de
Barcelona,Spain
GEORGEASIMENOS (cid:129) DepartmentofComputerScience,StanfordUniversity,Stanford,
CA,USA
JACQUELINE BATLEY (cid:129) Australian Centre for Plant Functional Genomics, School
ofLand,CropandFoodSciences,UniversityofQueensland,Brisbane,Australia
ENRIQUE BLANCO (cid:129) Departament de Gene`tica, Facultat de Biologia, Universitat de
Barcelona,Spain
JOANNA C. CHIU (cid:129) Department of Molecular Biology and Biochemistry, Rutgers
University,Piscataway,NJ,USA
MARK CLEMENT (cid:129) Department of Computer Science, Brigham Young University,
Provo,UT,USA
GLORIACORUZZI (cid:129) DepartmentofBiology,NewYorkUniversity,NewYork,NY,USA
KEITHA.CRANDALL (cid:129) DepartmentofBiology,BrighamYoungUniversity,Provo,UT,
USA
CHRISTOPHERJ.CREEVEY (cid:129) EMBLHeidelberg,Heidelberg,Germany
FREDERICDELSUC (cid:129) InstitutdesSciencesdel’Evolution deMontpellier(ISEM),UMR
5554-CNRS,Universite´ MontpellierII,Montpellier,France
ROB DESALLE (cid:129) Sackler Institute of Comparative Genomics, American Museum
ofNaturalHistoryNewYork,NY,USA
JEAN-FRANC¸OIS DUFAYARD (cid:129) Laboratoire d’Informatique, de Robotique et de Micro-
e´lectroniquedeMontpellier(LIRMM).UMR5506-CNRS,Universite´MontpellierII,
Montpellier,France
DAVIDEDWARDS (cid:129) AustralianCentreforPlantFunctionalGenomics,SchoolofLand,
CropandFoodSciences,UniversityofQueensland,Brisbane,Australia
MARYEGAN (cid:129) DepartmentofBiology,MontclairStateUniversity,Montclair,NJ,USA
SIMOND.W.FROST (cid:129) AntiviralResearchCenter,DepartmentofPathology,University
ofCaliforniaSanDiego,LaJolla,CA,USA
OLIVIERGASCUEL (cid:129) Laboratoired’Informatique,deRobotiqueetdeMicroe´lectronique
de Montpellier (LIRMM). UMR 5506-CNRS, Universite´ Montpellier I I, Montpel-
lier,France
STE´PHANEGUINDON (cid:129) Laboratoired’Informatique,deRobotiqueetdeMicroe´lectroni-
que de Montpellier (LIRMM). UMR 5506-CNRS, Universite´ Montpellier II,
Montpellier, France; Department of Statistics, University of Auckland. Auckland,
NewZealand
MICAH HAMADY (cid:129) Department of Computer Science, University of Colorado, Boulder,
CO,USA
xi