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D36D42 NucleicAcidsResearch,2013,Vol.41,Databaseissue Publishedonline27November2012

doi:10.1093/nar/gks1195

GenBank
Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi,
David J. Lipman, James Ostell y Eric W. Sayers*

NationalCenterforBiotechnologyInformation,NationalLibraryofMedicine,NationalInstitutesofHealth,
Building38A,8600RockvillePike,Bethesda,MD20894,USA

ReceivedSeptember28,2012;RevisedandAcceptedOctober29,2012

EXTRACTO secuencia(GSS),entero-genomeshotgun(WGS)y
otherhigh-throughputdatafromsequencingcentres.
GenBank’ (http://www.ncbi.nlm.nih.gov) es un com- TheU.S.PatentandTrademarkOfcealsocontributes

Descargado de
la base de datos de prehensive que contiene en público disponible
sequencesfromissuedpatents.GenBankparticipateswith
secuencias de nucleotide para casi 260000 especies theEuropeanMolecularBiologyLaboratoryNucleotide
formalmente descritas. Estas secuencias son SequenceDatabase(EMBL-banco),partoftheEuropean
obtenidas a través de sumisiones
principalmente de individuo NucleotideArchive(ENA)(2),andtheDNADataBank
laboratorios y sumisiones de la hornada de grandeofJapan - (DDBJ)(3)asapartnerintheInternational

http://nar.oxfordjournals.org/ en biblioteca de Wageningen UR el 19 de marzo de 2013

escale proyectos de sequencing, incluso el genoma entero NucleotideSequenceDatabaseCollaboration (INSDC).
escopeta (WGS) y ambiental prueba TheINSDCpartnersexchangedatadailytoensurethat ht
proyectos. La mayor parte de sumisiones son auniformandcomprehensivecollectionofsequencein- tp
hechas usando BankIt basado en la web o formationisavailableworldwide.NCBImakesthe ://
programas Sequin independientes, GenBank GenBankdataavailableatnocostovertheInternet,
y personal
asigna acceso números
throughFTPandawiderangeofweb-basedretrieval n
sobre recibo de datos. Intercambio de datos diario andanalysisservices
con el (4). ar
European Nucleotide Archive (ENA) y el Banco de
datos del ADN de Japón (DDBJ) aseguran la .oxf
cobertura mundial. GenBank es accesible a través RECENT DEVELOPMENTS
del NCBI Entrez el sistema de recuperación, que
integra datos del ADN principal y bases de datos de Submissionportal
la secuencia de la proteína junto con taxonomía,
genoma, correlación, estructura de la proteína e NCBIisintheprocessofcreatingauniedsubmission
información de la esfera y la literatura del diario del portalthatwillprovideasingleaccesspointfordatasub-
iCal biomed-vía PubMed. La RÁFAGA proporciona mitras(submit.ncbi.nlm.nih.gov).Submitterswillbeable
búsquedas de semejanzas de la secuencia de tocreateaccountsthatwilltrackanddisplayalloftheir
GenBank y otras bases de datos de la secuencia. submissionsandwillfacilitatecommunicationwith
Complete liberaciones bimensuales y las relevantNCBIstaff.WithrespecttoGenBank,the
actualizaciones diarias de la base de datos de
GenBank están disponibles portalnowsupportssubmissionsofwholegenome
por FTP. A acceso GenBank y su escopeta(WGS)andtranscriptomeshotgunassembly
servicios de análisis y recuperación relacionados, (TSA)sequencesand,inthenearfuture,completemicro-
comience en la página de inicio NCBI: bialgenomes.Submittersmaycontinuetousestandard
www.ncbi.nlm.nih.gov. Instrumentos de sumisin de GenBank (vØase
abajo)paraotroGenBanksubmissions.
INTRODUCCIÓN
Newsubmissionwizards
GenBank (1)
isacomprehensivepublicdatabaseofnu-cleotidesequencesands TheSequinprogram,apopulartoolforpreparingelec -
upportingbibliographicandbio - tronicsubmissions (seebelow), nowcontainsavarietyof
logicalannotation.GenBankisbuiltanddistributedby wizardstoassistuserswhensubmittingparticulartypes
theNationalCenterforBiotechnologyInformation(NCBI), ofsequences.ThecurrentreleaseofSequin(version12.21)
adivisionoftheNationalLibraryofMedicine (NLM), containswizardsforsubmittingviralsequences;uncul -
(NIH) locatedatthecampusoftheU.S.National turedsequences;rRNA,internaltranscribedspacer
InstitutesofHealthinBethesda,MD,losEE.UU. andrRNA-intergenicspacersequences (rRNA-ITS-IGS);
NCBIbuildsGenBankprimarilyfromthesubmission TSAsequencesandnon-rRNAintergenicspacersequences
ofsequencedatafromauthorsandfromthebulksubmis- (IGS).TheBankItwebsubmissiontoolalsohasaspecial
sionofexpressedsequencetag(EST),genomesurvey

*Towhomcorrespondenceshouldbeaddressed.Tel:+13014962475;Fax:+13014809241;Email:sayers@ncbi.nlm.nih.gov

PublishedbyOxfordUniversityPress2012.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(http://creativecommons.org/licenses/by-nc/3.0/),que
permitsnon-commercialreuse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.Forcommercialre-use,pleasecontact
journals.permissions@oup.com.
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Multilizer PDF Translator Free version - translation is limited to ~ 3 pages per translation.
functiontoassistwithsubmitting16SrRNAsequences.All
ofthesetoolsguideusersthroughtheprocessofsubmitting
therequireddataandalsoassistwithsequenceannotation.
WGSbrowser
WithinGenBank,WGSmasterrecords(seebelow)
containnosequencedata,butrathershowthedescriptive
informationandrangeofaccessionnumbersofthecontigs
submittedaspartofthatWGSproject.NCBIistransi-
tioningtoapointwherewewillnolongerassignGI
(GenInfo)numberstotheseindividualcontigs,particu-
larlyfordatafromlowcoverage,fragmentedorunanno-
tatedassembliesofeukaryoticgenomes.Contigswithout
GInumberswillnotbeavailablefromtheNucleotide
database;instead,usersmayviewtheserecordsinthe
WGSbrowserlinkedfromtheWGSfeatureofany
WGSmasterrecord.TheWGSbrowserprovidesthe
completedescriptiveinformationfromthemasterrecord
oftheproject,interactiveviewsoftheFASTAofevery
contigrecordandalsoprovideslinkstotheFTPlesfor
allthecontigsoftheentireproject.
NewTSAaccessions
NCBIisnowformattingandreleasingTSArecordssimi-
larlytowhathasbeendoneforWGSdata(seebelow).
LikeWGS,TSAprojectswillnowcontainamaster
record,inadditiontorecordsrepresentingeachofthe
assembledcontigs.TSAwillbeusingasimilaraccession
numberschemetoWGSaswell.LikeWGSaccessions,
thenewTSAaccessionshaveafour-letterprex,repre-
sentingtheTSAproject,followedbyatwo-digitversion
numberandasix-digitcontignumber.Forexample,
GAAA01000020iscontig20fromtherstversionof
TSAprojectGAAA.Inthefuture,theindividualTSA
contigswillnotbeindexedinEntrez,butwillbeavailable
intheWGSbrowser.TheTSAprojectmasterrecords
haveaccessionsthatbeginwiththefour-letterprex
followedbyeightzeroes(p.ej.GAAA00000000)andare
indexedintheNucleotidedatabase.
BothTSAandWGSrecordswillnowalsocontainan
AssemblyblockintheCOMMENTsectionoftheir
GenBankreports.TheAssemblyblockcontains,asavail-
able,informationabouttheassemblymethod,theassembly
name,thegenomecoverageachievedandthesequencing
technologyusedtogeneratethedata.AsampleAssembly
blockfromGAAA00000000isshownbelow:
##Assembly-Data-START##
AssemblyMethod ::Trinityv.r2011-07-13
AssemblyName ::LatCha_Muscle767971_v1.0
Cobertura ::590x
SequencingTechnology:: IlluminaHi-Seq
##Assembly-Data-END##
ORGANIZACIÓN DE LA BASE DE DATOS
GenBankdivisions
GenBankassignssequencerecordstovariousdivisions
basedeitheronthesourcetaxonomyorthesequencing
strategyusedtoobtainthedata.Thereare12taxonomic
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NucleicAcidsResearch,2013,Vol.41,Databaseissue D37
divisionsthatcorrespondroughlytothesourceorganisms
ofthesequencedata(BCT,ENV,INV,MAM,PHG,
PLN,PRI,VARA,SYN,UNA,VRL,VRT)and8func-
tionaldivisions(EST,GSS,HTC,HTG,F`CIL,STS,TSA,
WGS)thatcollectsequencesgeneratedbyaparticular
method.Thesizeandgrowthofthesedivisions,andof
GenBankasawhole,areshowninTable1. #Pages [3]
Secuencia-basedtaxonomy
Databasesequencesareclassiedandcanbequeriedusing
acomprehensivesequence-basedtaxonomy(www.ncbi.
nlm.nih.gov/taxonomy/)developedbyNCBIincollabor-
ationwithEMBL-BankandDDBJandwiththevaluable
assistanceofexternaladvisersandcurators(5).Almost
260000formallydescribedspeciesarerepresentedin
Descargado de
GenBankylasespeciessuperioresennon-WGS
GenBankdivisionsarelistedinTable2.
#Pages [3]
Sequenceidentiersandaccessionnumbers
EachGenBankrecord,consistingofbothasequenceand
itsannotations,isassignedauniqueidentiercalledan
http://nar.oxfordjournals.org/ en biblioteca de Wageningen UR el 19 de marzo de 2013
accessionnumberthatissharedacrossthethree bases de ht
datos que colaboran (GenBank, DDBJ, Banco
deEMBL-).Elnœmerodeaccesoapareceen tp
ACCESSIONlineofaGenBankrecordandremains ://
constantoverthelifetimeoftherecord,evenwhenthere n
isachangetothesequenceorannotation.Changestothe
sequencedataaretrackedbyanintegerextensionofthe ar
accessionnumber,andthis .oxf
Accession.version identier
appearsontheVERSIONlineoftheGenBankatle.
Otherchanges,suchasrevisedannotationsoradditionsof
publications,thatdonotaffectthesequencedatawillnot
resultinanewversionnumber.Theinitialversionofa
sequencehastheextension.1.Inaddition,eachversion
oftheDNAsequenceisalsoassignedauniqueNCBI
identiercalledaGInumberthatalsoappearsonthe
VERSIONlinefollowingthe Accession.version:
ACCESSIONAF000001
VERSIONAF000001.5GI:7274584
CadaunoSoldado nœmero corresponde a a œnico
Accession.version identier.Whenachangeismadetoa
sequenceinaGenBankrecord,anewGInumberisissued
totheupdatedsequenceandtheversionextensionofthe
Accession.version identierisincremented.Theaccession
numberfortherecordasawholeremainsunchanged,
andwillalwaysretrievethemostrecentversionofthe
record;theolderversionsremainavailableundertheold
identiers y su soldado original
Accession.versionnumbers.TheRevisionHistoryreport,availablefrom
theDisplaySettingsmenuonthesequencerecordview,
summarizesthevariousupdatesforthatGenBankrecord,
boththosethatresultedinanewversion (updatesto
sequencedata) andthosethatdidnot
(updatestonon-sequencedata).
Asimilarsystemtrackschangesinthecorresponding
proteintranslations.Theseidentiersappearasqualiers
forcodingsequence(CD)featuresintheFEATURES
portionofaGenBankentry,e.g./protein_id=AAF14809.1.
Proteinsequencetranslationsalsoreceivetheirown
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D38 NucleicAcidsResearch,2013,Vol.41,Databaseissue

Table1. GrowthofGenBankdivisions(nucleotidebasepairs)
a
Divisin Descripcin Release191(8/2012) Annualincrease(%)

Taxnomicdivisons
SYN SintØtico 928200038 494.2%
PHG Phages 84079451 34.4%
ENV Environmentalsamples 3374433548 32.1%
VRL Virus 1429464786 21.1%
BCT Bacterias 8439854434 21.0%
PLN Plantas 5481470133 15.6%
MAM Othermammals 863036872 6.9%
VRT Othervertebrates 2886594595 6.7%
PRI Primates 6317656773 3.3%
UNA Noanotado 127803 1.5%
VARA Roedores 4435106948 0.9%
INV Invertebrados 2493058927 ’ 1.7%
Functionaldivisions
TSA Transcriptomeshotgundata 5759588580 207.3%

Descargado de
WGS Entero-genomeshotgundata 308196411905 47.9%
F`CIL Patentedsequences 12118622726 8.6%
GSS Genomesurveysequences 21947780105 5.7%
EST Expressedsequencetags 40888051100 4.8%
HTG Alto-throughputgenomic 24359210558 0.1%
STS Sequencetaggedsites 636262446 0.1%

http://nar.oxfordjournals.org/ en biblioteca de Wageningen UR el 19 de marzo de 2013

HTC Alto-throughputcDNA 639165410 ’ 3.5%
ht
TOTAL AllGenBanksequences 451278177138 33.1%
tp
://
a
MeasuredrelativetoRelease185(8/2011).

n
Table2. ToporganismsinGenBank(Release191) GenBankaccessionnumberwillretrievethemostrecent ar
versionofthesequencedataforarecord,thesequence
Organismo Non-WGSbasepairs datareturnedfromsuchsearcheswillchangeovertimeif .oxf
therecordisupdated.Itisquitepossible,therefore,forthe
Homosapiens 16310774187
Musmusculus 9974977889
sequencedataretrievedtodaybyanaccessiontobediffer-
Rattusnorvegicus 6521253272 entfromthatdiscussedoranalysedinanarticlepublished
Bostaurus 5386258455 severalyearsago.Wethereforerecommendthatauthors
Zeamays 5062731057 includetheversionsufxwhencitingaGenBankaccession
Susscrofa 4887861860
Daniorerio 3120857462
(p.ej.AF000001.5),particularlyincaseswherethesequence
Strongylocentrotuspurpuratus 1435236534 coordinatesarecriticaltotheworkbeingdescribed.
Macacamulatta 1256203101
OryzasativaJaponicaGroup 1255686573
Xenopus(Silurana)tropicalis 1249938611 CONSTRUCCIÓN DE LA BASE DE DATOS
Nicotianatabacum 1197357811
Arabidopsisthaliana 1144226616 ThedatainGenBankandthecollaboratingdatabases,
Drosophilamelanogaster 1119965220 EMBL-BankandDDBJ,aresubmittedeitherbyindivid -
Pantroglodytes 1008323292 ualauthorstooneofthethreedatabasesorbysequencing
Vitisvinifera 999010073 centresasbatchesofEST,STS,GSS,HTC,TSA,WGSor
Canislupusfamiliaris 951238343
Glycinemax 906638854
HTGsequences.DataareexchangeddailywithDDBJ
Gallusgallus 899631338
andEMBL-BanksothatthedailyupdatesfromNCBI
Triticumaestivum 898689329 serversincorporatethemostrecentlyavailablesequence
datafromallsources.

uniqueGInumber,whichappearsasasecondqualieron
theCDSfeature:
/db_xref=GI:6513858
CitingGenBankrecords
BesidesbeingtheprimaryidentierofaGenBank
sequencerecord,GenBankaccessionsarealsothemost
efcientandreliablewaytociteasequencerecordinpub -
lications.Wecertainlyencouragesubmittersandother
authorstociteGenBankdatausingtheseaccessions.
However,asdiscussedabove,sincesearchingwitha
Directelectronicsubmission
VirtuallyallrecordsenterGenBankasdirectelectronic
sumisiones(www.ncbi.nlm.nih.gov/genbank/),conla
mayora de autores que usan los programas
BankIt o Sequin. Anonlinetable
(www.ncbi.nlm.nih.gov/guide/
howto/submit-sequence-data/)providesgeneralguidance
andlinkstoappropriatetoolsforsubmittingavarietyof
sequencedata.Manyjournalsrequireauthorswith
sequencedatatosubmitthedatatoapublicsequence
databaseasaconditionofpublication.GenBankstaff
canusuallyassignanaccessionnumbertoasequence

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submissionwithintwoworkingdaysofreceipt,anddoso
atarateof  3500perday.Theaccessionnumberservesas
confirmationthatthesequencehasbeensubmittedand
providesameansforreadersofarticlesinwhichthe
sequenceiscitedtoretrievethedata.Directsubmissions
receiveaqualityassurancereviewthatincludeschecksfor
vectorcontamination,propertranslationofcoding
regions,correcttaxonomyandcorrectbibliographiccit-
ations.AdraftoftheGenBankrecordispassedbackto
theauthorforreviewbeforeitentersthedatabase.
Authorsmayaskthattheirsequencesbekeptconfiden-
tialuntilthetimeofpublication.SinceGenBankpolicy
requiresthatthedepositedsequencedatabemadepublic
whenthesequenceoraccessionnumberispublished,
authorsareinstructedtoinformGenBankstaffofthe
publicationdateofthearticleinwhichthesequenceis
citedtoensureatimelyreleaseofthedata.Although
onlythesubmitterispermittedtomodifysequencedata
orannotations,allusersareencouragedtoreportlagsin
releasingdataorpossibleerrorsoromissionstoGenBank
atupdate@ncbi.nlm.nih.gov.
NCBIworkscloselywithsequencingcentrestoensure
timelyincorporationofbulkdataintoGenBankforpublic
release.GenBankoffersspecialbatchproceduresfor
large-scalesequencinggroupstofacilitatedatasubmis-
sion,includingtheprogram tbl2asn,describedatwww.
ncbi.nlm.nih.gov/genbank/tbl2asn2.html.
SubmissionusingBankIt
Aboutathirdofauthorsubmissionsarereceivedthrough
anNCBIweb-baseddatasubmissiontoolnamedBankIt.
UsingBankIt,authorsentersequenceinformationand
biologicalannotations,suchascodingregionsormRNA
features,directlyintoaseriesoftabbedformsthat
allowthesubmittertodescribethesequencefurther
withouthavingtolearnformattingrulesorcontrolled
vocabularies.Additionally,BankItallowssubmittersto
uploadsourceandannotationdatausingtab-delimited
tables.BeforecreatingadraftrecordintheGenBank
flatfileformatforthesubmittertoreview,BankItvalid-
atesthesubmissionsbyflaggingmanycommonerrorsand
checkingforvectorcontaminationusingavariantof
BLASTcalledVecscreen.
SubmissionusingSequinandtbl2asn
NCBIalsooffersastandalonemulti-platformsubmission
programcalledSequin(www.ncbi.nlm.nih.gov/projects/
Sequin/)thatcanbeusedinteractivelywithotherNCBI
sequenceretrievalandanalysistools.Sequinhandles
simplesequences(suchasasinglecDNA),phylogenetic
studies,populationstudies,mutationstudies,environmen-
talsampleswithorwithoutalignmentsandsequenceswith
complexannotation.Sequinhasconvenienteditingand
complexannotationcapabilitiesandcontainsanumber
ofbuilt-invalidationfunctionsforqualityassurance.
Sequinisabletoaccommodatesequencessuchasthe
5.6Mb E.coli genomeandreadinafullcomplementof
annotationsfromsimpletables.Themostrecentversion,
Sequin12.2,wasreleasedinJune2012andisavailablefor
Macintosh,PCandUnixcomputersviaanonymousFTP
atftp.ncbi.nlm.nih.gov/sequin.Onceasubmissionis
NucleicAcidsResearch,2013,Vol.41,Databaseissue D39
completed,submitterscanemailtheSequinfileto
gb-sub@ncbi.nlm.nih.gov.Submittersoflarge,heavily
annotatedgenomesareencouragedtousethecommand
linetool tbl2asn toconvertatableofannotations
generatedfromanannotationpipelineintoanASN.1
(AbstractSyntaxNotationOne)recordsuitableforsub-
missiontoGenBank.
SubmissionofBarcodesequences
TheConsortiumfortheBarcodeofLife(CBOLw.,
barcoding.si.edu/)isaninternationalinitiativetodevelop
DNAbarcodingasatoolforcharacterizingspeciesof
organismsusingashortDNAsequence.Foranimal
species,a648-basepairfragmentofthegeneforcyto-
chromeoxidasesubunitIisusedasthebarcode.The
plantandfungalcommunitiesareusingotherloci.
NCBIprovidesanonlinetool(BarSTool)forthebulk
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submissionofbarcodesequencestoGenBank(ww.
ncbi.nlm.nih.gov/WebSub/?tool=barcode)thatallows
userstouploadlescontainingabatchofsequences
withassociatedsourceinformation.Barcodesequences
canberetrievedfromtheNucleotidedatabasewiththe
querybarcode[keyword].
Additionalnotesonspecialdivisionsandrecordtypes
TranscriptomeShotgunAssembly(TSA)sequences
TheTSAdivisioncontainstranscriptomeshotgun
assemblysequencesthatareassembledfromsequencesde-
positedintheNCBITraceArchive,theSequenceRead
Archive(SRA)andtheESTdivisionofGenBank.
AlthoughneithertheTraceArchivenorSRAisapart
ofGenBank,theyarepartoftheINSDCandprovide
accesstothedataunderlyingtheseassemblies(4,6).TSA
recordshave‘TSA’astheirkeywordandcanberetrieved
withthequery‘tsa[properties]’.TSAcontinuestobeone
ofthemostrapidlygrowingdivisionsofGenBank,more
thantriplinginsizeoverthepastyear(Table1).
Environmentalsamplesequences(ENV)
TheENVdivisionofGenBankaccommodatessequences
obtainedviaenvironmentalsamplingmethodsinwhich
thesourceorganismisunknown.ManyENVsequences
arisefrommetagenomesamplesderivedfrommicrobiota
invariousanimaltissues,suchaswithinthegutorskin,
orfromparticularenvironments,suchasfreshwater
sediment,hotspringsorareasofminedrainage.Records
intheENVdivisioncontainENVinthekeywordeld
andusean/environmental_samplequalierinthesource
feature.Environmentalsamplesequencesaregenerally
submittedforwholemetagenomicshotgunsequencingex-
perimentsorsurveysofsequencesfromtargetedgenes,like
16SrRNA.NCBIcontinuestosupportBLASTsearches
(seebelow)ofmetagenomicENVsequences,butsequences
withinWGSprojectsarenowpartoftheWGSBLASTdatabase.
Whole-GenomeShotgunsequences
Whole-GenomeShotgun(WGS)sequencesappearin
GenBankasgroupsofsequence-overlapcontigscollected
underamasterWGSrecord.Eachmasterrecordrepresents
aWGSprojectandhasanaccessionnumberinthe
D40 NucleicAcidsResearch,2013,Vol.41,Databaseissue
Nucleotidedatabaseconsistingofafour-letterprefix
followedbyeightzeroesandaversionsuffixasfoundin
standardGenBankrecords.Thenumberofzeroesincreases
tonineforWGSprojectswithonemillionormorecontigs.
Masterrecordscontainnosequencedata;rather,theyare
linkedtotheirsetofindividualcontigsthatcanbeviewed
usingthenewWGSbrowser(seeabove).Contigrecords
haveaccessionsconsistingofthesamefour-letterprefixas
theirmasteraccession,followedbyatwo-digitversion
numberandasix-digitcontigID.Forexample,theWGS
accessionnumber‘AAAA02002744’isassignedtocontig
number‘002744’ofthesecondversionofproject‘AAAA’,
whoseaccessionnumberis‘AAAA00000000.2’.Currently,
thereare > 6000WGSsequencingprojects,manyofwhose
datahavebeenusedtobuildalmost12millionscaffoldsand
chromosomesforgenomeassemblies.Foracompletelistof
WGSprojectswithlinkstothedata,seewww.ncbi.nlm.nih.
gov/Traces/wgs/.
AlthoughWGSprojectsequencesmaybeannotated,
manylow-coveragegenomeprojectsdonotcontainanno-
tation.Becausethesesequenceprojectsareongoingand
incomplete,theseannotationsmaynotbetrackedfrom
oneassemblyversiontothenextandshouldbeconsidered
preliminary.Submittersofgenomicsequences,including
WGSsequences,areurgedtouseevidencetagsof
theform‘/experimental= CATEGORY:text’and‘/infer-
ence=CATEGORY:TYPEtext : ’,where TYPE isoneof
anumberofstandardinferencetypes, text consistsof
structuredtextandtheoptional CATEGORY labelis
oneofthefollowing:
COORDINATES—support for the annotated
coordinates
supportforabroadconceptof
DESCRIPTION—
functionsuchasthatbasedonphenotype,genetic
approach,biochemicalfunction,pathwayinformation,etc.
EXISTENCE—supportfortheknownorinferredexist-
enceoftheproduct.
Expressedsequencetags(ESTs)
ESTscontinuetobeamajorsourceofdataforgene
expressionandannotationstudies,andatalmost41
billionbasepairs,itremainsthelargestnon-WGS
divisioninGenBank.ESTdataareavailablefor
downloadfromftp.ncbi.nlm.nih.gov/repository/dbEST/
(7)aswellasfromtheGenBankFTPsite.Thedatain
dbESTareclusteredusingtheBLASTprogramsto
producetheUniGenedatabase(ww.ncbi.nlm.nih.gov/ unigene )of
5.8milliongene-orientedsequenceclusters
> ESTandGSSdivisionsofGenBankarestoredintheEST
representing142organisms(4).
High-throughputgenomic(HTG)andhigh-throughput
cDNA(HTC)sequences
TheHTGdivisionofGenBank(ww.ncbi.nlm.nih.gov/
genbank/htgs/)containsunnishedlarge-scalegenomic
records,whichareintransitiontoanishedstate( 8).
TheserecordsaredesignatedasbelongingtoPhases0to3
dependingonthequalityofthedata,withPhase3beingthe
nishedstate.OnreachingPhase3,HTGrecordsare
movedintotheappropriateorganismdivisionofGenBank.
TheHTCdivisionofGenBankcontainshigh-
throughputcDNAsequencesthatareofdraftquality
0
butmaycontain5untranslated regions(UTRs),
3UTRs,partialcodingregionsandintrons.HTCse-
0
quencesthatarefinishedandofhighqualityaremoved
totheappropriateorganismdivisionofGenBank.A
projectgeneratingHTCdataisdescribedin(9).
ThirdPartyAnnotation
ThirdPartyAnnotation(TPA)recordsaresequencean-
notationspublishedbysomeoneotherthantheoriginal
submitteroftheprimarysequencerecordinDDBJ/ENA/
GenBank(ww.ncbi.nlm.nih.gov/genbank/TPA).Eachof
thecurrent164000TPArecordsfallsintooneofthree
experimental
categories: ,inwhichcasethereisdirectex-
perimentalevidencefortheexistenceoftheannotated
inferential,inwhichcasetheexperimental
molecule; reassembly,wherethefocusis
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evidenceisindirect;and
onprovidingabetterassemblyoftherawreads.TPA
sequencesmaybecreatedbyassemblinganumberof
primarysequences.TheformatofaTPArecord(e.g.
BK000016)issimilartothatofaconventionalGenBank
recordbutincludesthelabel‘TPA_exp:’,‘TPA_inf:’or
‘TPA_reasm:’atthebeginningofeachDefinitionLine
aswellascorrespondingkeywords.TPAexperimental
andinferentialrecordsalsocontainaPrimaryblockthat
providesthebaserangesandidentifierforthesequences
usedtobuildtheTPA.TPAsequencesarenotreleasedto
thepublicuntiltheiraccessionnumbersorsequencedata
andannotationappearinapeer-reviewedbiological
journal.TPAsubmissionstoGenBankmaybemade
usingeitherBankItorSequin.
Contig(CON)recordsforassembliesofsmallerrecords
WithinGenBank,CONrecordsareusedtorepresentvery
longsequences,suchasaeukaryoticchromosome,where
thesequenceisnotcompletebutconsistsofseveralcontig
recordswithuncharacterizedgapsbetweenthem.Rather
thanlistingthesequenceitself,CONrecordscontain
assemblyinstructionsinvolvingtheseveralcomponentse-
quences.AnexampleofsuchaCONrecordisCM000663
forhumanchromosome1.
RETRIEVING GENBANK DATA
TheEntrezsystem
ThesequencerecordsinGenBankareaccessiblethrough
theNCBIEntrezretrievalsystem(4).Recordsfromthe
andGSSdatabases,whereasallotherGenBankrecords
arestoredintheNucleotidedatabase(Table3).GenBank
sequencesthatarepartofpopulationorphylogeneticstudies
are also collected together in the PopSet
database,andconceptualtranslationsofCDSsequences
annotatedonGenBankrecordsareavailableinthe
Proteindatabase.Eachofthesedatabasesislinkedto
thescientificliteratureinPubMedandPubMedCentral.
AdditionalinformationaboutconductingEntrezsearches
isfoundintheNCBIHelpManual(www.ncbi.nlm.nih.
gov/books/NBK3831/)andlinkstorelatedtutorialsare
providedontheNCBIEducationpage(www.ncbi.nlm.
nih.gov/education/).

Table3. RetrievaldatabasescontainingGenBankdata
Division Entrez
database
BCT,ENV,INV,MAM,PHG,PLN, nucleotide
PRI,ROD,SYN,UNA,VRL,VRT
EST est
GSS gss
HTC nucleotide
HTG nucleotide
PAT nucleotide
STS nucleotide
TSA nucleotide
WGS nucleotide
Associatingsequencerecordswithsequencingprojects
TheabilitytoidentifyallGenBankrecordssubmittedbya
specificgrouporthosewithaparticularfocus,suchas
metagenomicsurveys,isessentialfortheanalysisof
largevolumesofsequencedata.Theuseoforganismor
submitternamesasameanstodefinesuchasetofse-
quencesisunreliable.TheBioProjectdatabase(www.
ncbi.nlm.nih.gov/bioproject),developedatNCBIandsub-
sequentlyadoptedacrosstheINSDC,allowssubmittersto
registerlarge-scalesequencingprojectsunderaunique
projectidentifier,enablingreliablelinkagebetween
sequencingprojectsandthedatatheyproduce(10).
BioProjectincludespointerstodatafromawidevariety
ofprojectsdepositedinanyNCBIprimarydataarchive.
Sequencingprojectsfocusongenomes,metagenomes,
transcriptomes,comparativegenomicsaswellasonpar-
ticularloci,suchas16SribosomalRNA.A‘DBLINK’
lineappearinginGenBankflatfilesidentifiesthe
sequencingprojectswithwhichaGenBanksequence
recordisassociated.Inaddition,sequencerecordsmay
nowhavealinktotheBioSampledatabase(10)that
providesadditionalinformationaboutthebiologicalma-
terialsusedinthestudythatproducedthesequencedata.
Suchstudiesincludegenome-wideassociationstudies,
high-throughputsequencing,microarraysandepigenomic
analyses.Asanexample,theTSAprojectGAAA(see
above)containsDBLINKlinesthatassociatethe
GenBanksequencerecordwithBioProjectrecord
PRJNA54005andBioSamplerecordSRS283232,aswell
astheSRArecordcontainingtherawdata,SRR401852:
BioProject:PRJNA77699
BioSample:SRS283232 MAILING ADDRESS
SequenceReadArchive:SRR401852
AnotherexampleistheHumanMicrobiomeProjec GenBank,
t Information,Building45,Room6AN12D-37,45Center
(HMP)thatisrepresentedbytheumbrellaBioProj
ect 43021 Drive,Bethesda,MD20892,USA.
(w.ncbi.nlm.nih.gov/bioproject/43021).
Users
canthen“ndsequencedatabyfollowinglinkstothevarioussubprojectslistedonthisrecord.
ELECTRONIC ADDRESSES
BLASTsequence-similaritysearching
Sequence-similaritysearchesarethemostfundamental
andfrequenttypeofanalysisperformedonGenBank
data.NCBIofferstheBLASTfamilyofprograms
(blast.ncbi.nlm.nih.gov)todetectsimilaritiesbetweena
querysequenceanddatabasesequences(11,12).BLAST
NucleicAcidsResearch,2013,Vol.41,Databaseissue D41
searchesmaybeperformedontheNCBIwebsite(13)
orbyusingasetofstandaloneprogramsdistributed
BLAST
database byFTP(4).Table3displaystheappropriateBLASTdata-
basesforthevariousdivisionsofGenBank.
nr
ObtainingGenBankbyFTP
est
gss NCBIdistributesGenBankreleasesinthetraditionalflat
nr fileformataswellasintheASN.1formatusedforinternal
htg maintenance.ThefullbimonthlyGenBankreleasealong
pat
dbsts
withthedailyupdates,whichincorporatesequencedata
tsa fromEMBL-BankandDDBJ,isavailablebyanonymous
wgs FTPfromNCBIat ftp.ncbi.nlm.nih.gov/genbank.
GenBankisalsoavailableforhigh-speeddownload
usinganAsperaclientatwww.ncbi.nlm.nih.gov/public/.
Thefullreleaseinflatfileformatisavailableasasetof
compressedfileswithanon-cumulativesetofupdatesat
Downloaded from http://nar.oxfordjournals.org/ at Wageningen UR Library on March 19, 2013
ftp.ncbi.nlm.nih.gov/genbank/daily-nc/.Forconvenience
infiletransfer,thedataarepartitionedintomultiple
files;forrelease191,thereare1852filesrequiring
604GBofuncompresseddiskstorage.Ascriptis provided
in ftp.ncbi.nlm.nih.gov/genbank/tools/ to
convertasetofdailyupdatesintoacumulativeupdate.
FOR MORE INFORMATION
AdditionalinformationaboutGenBankisavailableon
themainGenBankwebpage(www.ncbi.nlm.nih.gov/
genbank)andtheEntrezSequencesHelpManual(www.
ncbi.nlm.nih.gov/books/NBK44864/). The NCBI
Educationpage(www.ncbi.nlm.nih.gov/Education/)lists
linkstoNCBIdocumentation,tutorialsandeducational
toolsalongwithlinkstooutreachinitiativesincluding
DiscoveryWorkshops,webinarsandupcomingconfer-
enceexhibits.NCBIprovidesupdatestoGenBankand
otherresourcesbyRSS(www.ncbi.nlm.nih.gov/feed/)
andonTwitterandFacebook(linksareinthecommon
footerofNCBIpages).Usersmayalsowanttoconsultthe
bionetGenBanknewsgroup(www.bio.net/bionet/mm/
genbankb/).ThisnewsgroupisnotmanagedbyNCBI,
butNCBIstaffareregularcontributors.Finally,a
completedescriptionofeachGenBankreleaseis
providedinthegbrel.txtfiledistributedaspartofthe
release,andanarchiveofthesefilesisprovidedatftp.
ncbi.nlm.nih.gov/genbank/release.notes/.
National Center for Biotechnology
www.ncbi.nlm.nih.gov—NCBIHomePage.
gb-sub@ncbi.nlm.nih.gov—Submission of sequence
datatoGenBank.
update@ncbi.nlm.nih.gov—Revisionsto,ornotifica-
tionofreleaseof,‘confidential’GenBankentries.
info@ncbi.nlm.nih.gov—Generalinformationabout
NCBIresources.
D42 NucleicAcidsResearch,2013,Vol.41,Databaseissue
CITING GENBANK
IfyouusetheGenBankdatabaseinyourpublished
research,weaskthatthisarticlebecited.
FUNDING
Fundingforopenaccesscharge:IntramuralResearch
ProgramoftheNationalInstitutesofHealth;National
LibraryofMedicine.
Conflictofintereststatement .Nonedeclared.
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