Gene Prediction: Methods and Protocols

286 Pages·2019·7.317 MB·English

by  Martin Kollmar

Methods in
Molecular Biology 1962
Martin Kollmar Editor
Gene
Prediction
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Gene Prediction
Methods and Protocols
Edited by
Martin Kollmar
Group Systems Biology of Motor Proteins, Department NMR-based Structural Biology,
Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
Editor
MartinKollmar
GroupSystemsBiologyofMotorProteins
DepartmentNMR-basedStructuralBiology
Max-Planck-InstituteforBiophysicalChemistry
Goettingen,Germany
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9172-3 ISBN978-1-4939-9173-0 (eBook)
https://doi.org/10.1007/978-1-4939-9173-0
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Preface
Since the application of new high-throughput sequencing methods (next-generation
sequencing) to genome sequencing, the number of sequenced eukaryotic genomes is
increasing more and more rapidly. Several large-scale sequencing projects of thousands of
specieshavealreadybeenstartedyearsago,suchasthe1kfungiproject,the“Genome10k”
project(10,000vertebrates),thei5kproject(5000insects),andthe959nematodesproject.
While genome sequencing steps from record to record, progress in genome annotation is
developing slowly. Despite considerable experimental and bioinformatics efforts, even the
annotationofthehumangenomehasnotbeenfinishedyet.Forotherspecies,thequalityof
theannotationsissignificantlyworse.Inadditiontotheintrinsicincompletenessofgenome
annotations, annotations are currently only available for a small part of all sequenced
genomes. Annotations are usually only updated for the most important model species.
Formanyspecies,onlytheinitialgenomeannotationsareavailable,althoughincorporation
ofnewdata(e.g.,transcriptsequencing)andapplicationofnewapproachescouldconsider-
ablyimproveannotations.
Improvements in genome annotations have a direct positive effect on all downstream
analysesaswellasdiverseapplicationsinmedicine,biology,biotechnology,andagriculture.
Thisvolumeintroducessoftwareforgenepredictionwithfocusoneukaryoticgenomes.The
primaryaudienceareresearchersandresearchgroupsworkingontheassemblyandannota-
tion of single species or small groups of species. Such groups usually do not have access to
advancedandcomplexannotationpipelines,whichareinusebysomelarge-scalesequencing
centers, and usually do not have particular expertise in gene prediction software. Also, the
focusofsuchgroupsisoftenonaparticularbiologicalaspectthatcanwellbeexplainedwith
just a very preliminary and partially incomplete genome annotation. The protocols
describedinthisvolumeshouldenablethesegroupstoconsiderablyimproveandcomplete
their genome annotations to be useful for a wider research community. Re-annotation of
longavailablegenomeassembliesshouldalsobesimplified.Availablesoftwarealsocontains
optionsandparametersthatareoftenhiddentothenoviceoroccasionaluser.Chapterswill
explainsoftwareandwebserver usageasappliedintypicalusecases,writteninthespiritof
theseries,whichaimstoprovidepracticalguidanceandtroubleshootingadvice.
Goettingen,Germany MartinKollmar
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 tRNAscan-SE:Searchingfor tRNAGenesinGenomicSequences............. 1
PatriciaP.ChanandToddM.Lowe
2 PredictingRNAFamiliesinNucleotideSequences
UsingStructRNAfinder.................................................. 15
ViniciusMaracaja-Coutinho,Rau´lArias-Carrasco,
HelderI.Nakaya,andVictorAliaga-Tobar
3 StructuralandFunctionalAnnotationofEukaryotic
GenomeswithGenSAS.................................................. 29
JodiL.Humann,TaeinLee,StephenFicklin,andDorrieMain
4 PracticalGuideforFungalGenePredictionfromGenome
AssemblyandRNA-SeqReadsbyFunGAP ................................ 53
ByoungnamMinandIn-GeolChoi
5 Whole-GenomeAnnotationwithBRAKER ................................ 65
KatharinaJ.Hoff,AlexandreLomsadze,MarkBorodovsky,
andMarioStanke
6 EuGene:AnAutomatedIntegrativeGeneFinder forEukaryotes
andProkaryotes ........................................................ 97
ErikaSallet,Je´roˆmeGouzy,andThomasSchiex
7 ChemGenome2.1:AnAbInitioGenePredictionSoftware................... 121
AkhileshMishra,PriyankaSiwach,PoonamSinghal,andB.Jayaram
8 Multi-GenomeAnnotationwithAUGUSTUS.............................. 139
StefanieNachtweideandMarioStanke
9 GeMoMa:Homology-BasedGenePredictionUtilizingIntron
PositionConservationandRNA-seqData ................................. 161
JensKeilwagen,FrankHartung,andJanGrau
10 CodingExon-StructureAwareRealigner(CESAR):UtilizingGenome
AlignmentsforComparativeGeneAnnotation ............................. 179
ViragSharmaandMichaelHiller
11 PredictingGenesinCloselyRelatedSpecieswithScipioandWebScipio ....... 193
MartinKollmar
12 AnABlast:Re-searchingforProtein-CodingSequencesinGenomicRegions... 207
AlejandroRubio,CarlosS.Casimiro-Soriguer,PabloMier,
MiguelA.Andrade-Navarro,Andre´sGarz(cid:1)on,JuanJimenez,
andAntonioJ.Pe´rez-Pulido
13 GeneratingPublication-ReadyProkaryoticGenomeAnnotations
withDFAST ........................................................... 215
YasuhiroTanizawa,TakatomoFujisawa,MasanoriArita,
andYasukazuNakamura
vii
viii Contents
14 BUSCO:AssessingGenomeAssemblyandAnnotationCompleteness......... 227
MathieuSeppey,Mose` Manni,andEvgenyM.Zdobnov
15 EvaluatingGenomeAssembliesandGeneModelsUsinggVolante............ 247
OsamuNishimura,YuichiroHara,andShigehiroKuraku
16 ChoosingtheBestGenePredictionswithGeneValidator .................... 257
IsmailMoghul,AnuragPriyam,andYannickWurm
17 COGNATE:ComparativeGeneAnnotationCharacterizer................... 269
JeanneWilbrandt
Index ...................................................................... 283
Contributors
VICTORALIAGA-TOBAR (cid:1) FacultaddeCienciasQuı´micasyFarmace´uticas,AdvancedCenter
forChronicDiseases—ACCDiS,UniversidaddeChile,Santiago,Chile;Programade
DoctoradoenGen(cid:1)omicaIntegrativa,Vicerrectorı´adeInvestigaci(cid:1)on,UniversidadMayor,
Santiago,Chile
MIGUELA.ANDRADE-NAVARRO (cid:1) FacultyofBiology,JohannesGutenbergUniversityMainz,
Mainz,Germany
RAU´LARIAS-CARRASCO (cid:1) FacultaddeCienciasQuı´micasyFarmace´uticas,AdvancedCenter
forChronicDiseases—ACCDiS,UniversidaddeChile,Santiago,Chile;Programade
DoctoradoenGen(cid:1)omicaIntegrativa,Vicerrectorı´adeInvestigaci(cid:1)on,UniversidadMayor,
Santiago,Chile
MASANORIARITA (cid:1) DepartmentofInformatics,NationalInstituteofGenetics,Shizuoka,
Japan;RIKENCenter forSustainableResourceScience,Yokohama,Kanagawa,Japan
MARKBORODOVSKY (cid:1) JointGeorgiaTechandEmoryUniversityWallaceHCoulter,
DepartmentofBiomedicalEngineering,Atlanta,GA,USA;SchoolofComputational
ScienceandEngineering,Atlanta,GA,USA;MoscowInstituteofPhysicsandTechnology,
Dolgoprudny,MoscowRegion,Russia
CARLOSS.CASIMIRO-SORIGUER (cid:1) FacultaddeCienciasExperimentales(A´readeGene´tica),
CentroAndaluzdeBiologı´adelDesarrollo(CABD,UPO-CSIC),UniversidadPablode
Olavide,Sevilla,Spain
PATRICIAP.CHAN (cid:1) DepartmentofBiomolecularEngineering,UniversityofCalifornia
SantaCruz,SantaCruz,CA,USA
IN-GEOLCHOI (cid:1) DepartmentofBiotechnology,CollegeofLifeSciencesandBiotechnology,
KoreaUniversity,Seoul,SouthKorea
STEPHENFICKLIN (cid:1) DepartmentofHorticulture,WashingtonStateUniversity,Pullman,
WA,USA
TAKATOMOFUJISAWA (cid:1) DepartmentofInformatics,NationalInstituteofGenetics,Shizuoka,
Japan
ANDRE´SGARZO´N (cid:1) FacultaddeCienciasExperimentales(A´readeGene´tica),Centro
AndaluzdeBiologı´adelDesarrollo(CABD,UPO-CSIC),UniversidadPablodeOlavide,
Sevilla,Spain
JE´ROˆMEGOUZY (cid:1) LaboratoiredesInteractionsPlantes-Microorganismes(LIPM),Universite´
deToulouse,INRA,CNRS,Castanet-Tolosan,France
JANGRAU (cid:1) InstituteofComputerScience,MartinLutherUniversityHalle-Wittenberg,
Halle(Saale),Germany
YUICHIROHARA (cid:1) LaboratoryforPhyloinformatics,RIKENCenter forBiosystemsDynamics
Research(BDR),Kobe,Japan
FRANKHARTUNG (cid:1) InstituteforBiosafetyinPlantBiotechnology,JuliusKu¨hn-Institut(JKI),
FederalResearchCentreforCultivatedPlants,Quedlinburg,Germany
MICHAELHILLER (cid:1) MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,
Germany;MaxPlanckInstitutefor thePhysicsofComplexSystems,Dresden,Germany;
Center forSystemsBiology,Dresden,Germany
KATHARINAJ.HOFF (cid:1) UniversityofGreifswald,InstituteofMathematicsandComputer
Science,Greifswald,Germany
ix
x Contributors
JODI L.HUMANN (cid:1) DepartmentofHorticulture,WashingtonStateUniversity,Pullman,
WA,USA
B.JAYARAM (cid:1) SupercomputingFacilityforBioinformatics andComputationalBiology,
IndianInstituteofTechnologyDelhi,NewDelhi,India;KusumaSchoolofBiological
Sciences,IndianInstituteofTechnologyDelhi,NewDelhi,India;Departmentof
Chemistry,IndianInstituteofTechnologyDelhi,NewDelhi,India
JUANJIMENEZ (cid:1) FacultaddeCienciasExperimentales(A´readeGene´tica),CentroAndaluz
deBiologı´adelDesarrollo(CABD,UPO-CSIC),UniversidadPablodeOlavide,Sevilla,
Spain
JENSKEILWAGEN (cid:1) InstituteforBiosafetyinPlantBiotechnology,JuliusKu¨hn-Institut(JKI),
FederalResearchCentreforCultivatedPlants,Quedlinburg,Germany
MARTINKOLLMAR (cid:1) GroupSystemsBiologyofMotorProteins,DepartmentofNMR-Based
StructuralBiology,Max-Planck-InstituteforBiophysicalChemistry,Goettingen,Germany
SHIGEHIRO KURAKU (cid:1) LaboratoryforPhyloinformatics, RIKENCenter forBiosystems
DynamicsResearch(BDR),Kobe,Japan
TAEINLEE (cid:1) DepartmentofHorticulture,WashingtonStateUniversity,Pullman,WA,USA
ALEXANDRELOMSADZE (cid:1) JointGeorgiaTechandEmoryUniversityWallaceHCoulter
DepartmentofBiomedicalEngineering,Atlanta,GA,USA
TODDM.LOWE (cid:1) DepartmentofBiomolecularEngineering,UniversityofCaliforniaSanta
Cruz,SantaCruz,CA,USA
DORRIE MAIN (cid:1) DepartmentofHorticulture,WashingtonStateUniversity,Pullman,WA,
USA
MOSE` MANNI (cid:1) DepartmentofGeneticMedicineandDevelopment,SwissInstituteof
Bioinformatics,UniversityofGenevaMedicalSchool,Geneva,Switzerland
VINICIUS MARACAJA-COUTINHO (cid:1) FacultaddeCienciasQuı´micasyFarmace´uticas,
AdvancedCenterforChronicDiseases—ACCDiS,UniversidaddeChile,Santiago,Chile;
BeagleBioinformatics,Santiago,Chile;InstitutoVandique,Joa˜oPessoa,Brazil
PABLO MIER (cid:1) FacultyofBiology,JohannesGutenbergUniversityMainz,Mainz,Germany
BYOUNGNAMMIN (cid:1) DepartmentofBiotechnology,CollegeofLifeSciencesandBiotechnology,
KoreaUniversity,Seoul,SouthKorea
AKHILESHMISHRA (cid:1) SupercomputingFacilityforBioinformaticsandComputationalBiology,
IndianInstituteofTechnologyDelhi,NewDelhi,India;KusumaSchoolofBiological
Sciences,IndianInstituteofTechnologyDelhi,NewDelhi,India
ISMAILMOGHUL (cid:1) UCLCancerInstitute,UniversityCollegeLondon,London,UK
STEFANIENACHTWEIDE (cid:1) InstituteofMathematicsandComputerScience,Universityof
Greifswald,Greifswald,Germany
YASUKAZUNAKAMURA (cid:1) DepartmentofInformatics,NationalInstituteofGenetics,Shizuoka,
Japan
HELDERI.NAKAYA (cid:1) DepartmentofClinicalandToxicologicalAnalyses,Schoolof
PharmaceuticalSciences,UniversityofSa˜oPaulo,Sa˜oPaulo,Brazil
OSAMUNISHIMURA (cid:1) LaboratoryforPhyloinformatics, RIKENCenter forBiosystems
DynamicsResearch(BDR),Kobe,Japan
ANTONIO J.PE´REZ-PULIDO (cid:1) FacultaddeCienciasExperimentales(A´readeGene´tica),
CentroAndaluzdeBiologı´adelDesarrollo(CABD,UPO-CSIC),UniversidadPablode
Olavide,Sevilla,Spain
ANURAGPRIYAM (cid:1) SchoolofBiologicalandChemicalSciences,QueenMaryUniversityof
London,London,UK
Contributors xi
ALEJANDRORUBIO (cid:1) FacultaddeCienciasExperimentales(A´readeGene´tica),Centro
AndaluzdeBiologı´adelDesarrollo(CABD,UPO-CSIC),UniversidadPablodeOlavide,
Sevilla,Spain
ERIKASALLET (cid:1) LaboratoiredesInteractionsPlantes-Microorganismes(LIPM),Universite´de
Toulouse,INRA,CNRS,Castanet-Tolosan,France
THOMASSCHIEX (cid:1) Unite´deMathe´matiquesetInformatiqueApplique´esdeToulouse(MIAT),
Universite´deToulouse,INRA,Castanet-Tolosan,France
MATHIEUSEPPEY (cid:1) DepartmentofGeneticMedicineandDevelopment,SwissInstituteof
Bioinformatics,UniversityofGenevaMedicalSchool,Geneva,Switzerland
VIRAGSHARMA (cid:1) MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,
Germany;MaxPlanckInstitutefor thePhysicsofComplexSystems,Dresden,Germany;
Center forSystemsBiology,Dresden,Germany;CRTD-DFGCenter forRegenerative
TherapiesDresden,CarlGustavCarusFacultyofMedicine,TechnischeUniversita€t
Dresden,Dresden,Germany;PaulLangerhansInstituteDresden(PLID)oftheHelmholtz
CenterMunichatUniversityHospitalCarlGustavCarusandFacultyofMedicine,
TechnischeUniversita€tDresden,Dresden,Germany;GermanCenterforDiabetesResearch
(DZD),Munich,Germany
POONAMSINGHAL (cid:1) SupercomputingFacilityforBioinformaticsandComputationalBiology,
IndianInstituteofTechnologyDelhi,NewDelhi,India
PRIYANKASIWACH (cid:1) SupercomputingFacilityforBioinformaticsandComputationalBiology,
IndianInstituteofTechnologyDelhi,NewDelhi,India;DepartmentofBiotechnology,
ChaudharyDeviLalUniversity,Sirsa,Haryana,India
MARIOSTANKE (cid:1) InstituteofMathematicsandComputerScience,UniversityofGreifswald,
Greifswald,Germany
YASUHIROTANIZAWA (cid:1) DepartmentofInformatics,NationalInstituteofGenetics,Shizuoka,
Japan
JEANNEWILBRANDT (cid:1) Center forMolecularBiodiversityResearch,ZoologicalResearch
MuseumAlexanderKoenig(ZFMK),Bonn,Germany
YANNICKWURM (cid:1) SchoolofBiologicalandChemicalSciences,QueenMaryUniversityof
London,London,UK
EVGENYM.ZDOBNOV (cid:1) DepartmentofGeneticMedicineandDevelopment,SwissInstituteof
Bioinformatics,UniversityofGenevaMedicalSchool,Geneva,Switzerland