引用 NCBI常见术语.docx

引用 NCBI常见术语.docx

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引用NCBI常见术语

3-Dor3D

Three-dimensional.

Accessionnumber

AnAccessionnumberisauniqueidentifiergiventoasequencewhenitissubmittedtooneoftheDNArepositories（GenBank,EMBL,DDBJ）.Theinitialdepositionofasequencerecordisreferredtoasversion1.Ifthesequenceisupdated,theversionnumberisincremented,buttheAccessionnumberwillremainconstant.

allele

Oneofthevariantformsofageneataparticularlocusonachromosome.Differentallelesproducevariationininheritedcharacteristicssuchashaircolororbloodtype.Inanindividual,oneformoftheallele（thedominantone）maybeexpressedmorethananotherform（therecessiveone）.When“genes”areconsideredsimplyassegmentsofanucleotidesequence,allelereferstoeachofthepossiblealternativenucleotidesataspecificpositioninthesequence.Forexample,aCTpolymorphismsuchasCCT[C/T]CCATwouldhavetwoalleles:

CandT.

API

ApplicationProgrammingInterface.AnAPIisasetofroutinesthatanapplicationusestorequestandcarryoutlower-levelservicesperformedbyacomputer'soperatingsystem.Forcomputersrunningagraphicaluserinterface,anAPImanagesanapplication'swindows,icons,menus,anddialogboxes.

ASN.1

AbstractSyntaxNotation1isaninternationalstandarddata-representationformatusedtoachieveinteroperabilitybetweencomputerplatforms.Itallowsforthereliableexchangeofdataintermsofstructureandcontentbycomputerandsoftwaresystemsofalltypes.

BAC

BacterialArtificialChromosome.ABACisalargesegmentofDNA（100,000–200,000bp）fromanotherspeciesclonedintobacteria.OncetheforeignDNAhasbeenclonedintothehostbacteria,manycopiesofitcanbemade.

bitscore

ThevalueS′isderivedfromtherawalignmentscoreSinwhichthestatisticalpropertiesofthescoringsystemusedhavebeentakenintoaccount.Bynormalizingarawscoreusingtheformula:

a“bitscore”S′isattained,whichhasastandardsetofunits,andwhereKandlambdaarethestatisticalparametersofthescoringsystem.Becausebitscoreshavebeennormalizedwithrespecttothescoringsystem,theycanbeusedtocomparealignmentscoresfromdifferentsearches.

BLAST

BasicLocalAlignmentSearchTool（Altschuletal.,JMolBiol215:

403-410;1990）.Asequencecomparisonalgorithmthatisoptimizedforspeedandusedtosearchsequencedatabasesforoptimallocalalignmentstoaquery.SeetheBLASTchapter（Chapter15）orthetutorialorthenarrativeguidetoBLAST.

blastn

nucleotide–nucleotideBLAST.blastntakesnucleotidesequencesinFASTAformat,GenBankAccessionnumbers,orGInumbersandcomparesthemagainsttheNCBINucleotidedatabases.

blastp

protein–proteinBLAST.blastptakesproteinsequencesinFASTAformat,GenBankAccessionnumbers,orGInumbersandcomparesthemagainsttheNCBIProteindatabases.

BLAT

ADNA/Proteinsequenceanalysisprogramtoquicklyfindsequencesof95%andgreatersimilarityoflength40basesormore.Itmaymissmoredivergentorshortersequencealignments.BLATonproteinsfindssequencesof80%andgreatersimilarityoflength20aminoacidsormore.BLATisnotBLAST.（SeetheBLATwebpage.）

BLOB

BinaryLargeObject（orbinarydataobject）.BLOBreferstoalargepieceofdata,suchasabitmap.ABLOBischaracterizedbylargefieldvalues,anunpredictabletablesize,anddatathatareformlessfromtheperspectiveofaprogram.ItisalsoakeyworddesignatingtheBLOBstructure,whichcontainsinformationaboutablockofdata.

build

Arunofthegenomeassemblyandannotationprocessofthesetofproductsgeneratedbythatrun.

CCAP

CancerChromosomeAberrationProject.CCAPwasdesignedtoexpeditethedefinitionanddetailedcharacterizationofthedistinctchromosomalalterationsthatareassociatedwithmalignanttransformation.TheprojectisacollaborationamongtheNCI,theNCBI,andnumerousresearchlabs.

CD

ConservedDomain.CDreferstoadomain（adistinctfunctionaland/orstructuralunitofaprotein）thathasbeenconservedduringevolution.Duringevolution,changesatspecificpositionsofanaminoacidsequenceintheproteinhaveoccurredinawaythatpreservethephysico-chemicalpropertiesoftheoriginalresidues,andhencethestructuraland/orfunctionalpropertiesofthatregionoftheprotein.

CDART

ConservedDomainArchitectureRetrievalTool.Whengivenaproteinquerysequence,CDARTdisplaysthefunctionaldomainsthatmakeuptheproteinandlistsproteinswithsimilardomainarchitectures.Thefunctionaldomainsforasequencearefoundbycomparingtheproteinsequencetoadatabaseofconserveddomainalignments,CDDusingRPS-BLAST.

CDD

ConservedDomainDatabase.Thisdatabaseisacollectionofsequencealignmentsandprofilesrepresentingproteindomainsconservedduringmolecularevolution.

cDNA

complementaryDNA.ADNAsequenceobtainedbyreversetranscriptionofamessengerRNA（mRNA）sequence.

CDS

codingregion,codingsequence.CDSreferstotheportionofagenomicDNAsequencethatistranslated,fromthestartcodontothestopcodon,inclusively,ifcomplete.ApartialCDSlackspartofthecompleteCDS（itmaylackeitherorboththestartandstopcodons）.SuccessfultranslationofaCDSresultsinthesynthesisofaprotein.

CEPH

Centred'EtudeduPolymorphismHumain

CGAP

CancerGenomeAnatomyProject.CGAPisaninterdisciplinaryprogramtoidentifythehumangenesexpressedindifferentcancerousstates,basedoncDNA（EST）libraries,andtodeterminethemolecularprofilesofnormal,precancerous,andmalignantcells.TheprojectisacollaborationamongtheNCI,theNCBI,andnumerousresearchlabs.

CGH

ComparativeGenomicHybidization.CGHisafluorescentmolecularcytogenetictechniquethatidentifieschromosomalaberrationsandmapsthesechangestometaphasechromosomes.CGHcanbeusedtogenerateamapofDNAcopynumberchangesintumorgenomes.CGHisbasedonquantitativetwo-colorfluorescenceinsituhybridization（FISH）.DNAextractedfromtumorcellsislabeledinonecolor（e.g.,green）andmixedina1:

1ratiowithDNAfromnormalcells,whichislabeledinadifferentcolor（e.g.,red）.Themixtureisthenappliedtonormalmetaphasechromosomes.Portionsofthegenomethatareequallyrepresentedinnormalandtumorcellswillappearorange,regionsthataredeletedinthetumorsamplerelativetothenormalsamplewillappearred,andregionsthatarepresentinhighercopynumberinthetumorsample（becauseofamplification）willappeargreen.Specialimageanalysistoolsarenecessarytoquantitatetheratioofgreen-to-redfluorescencetodeterminewhetheragivenregionismorehighlyrepresentedinthenormalorinthetumorsample.

CGI

CommonGatewayInterface.AmechanismthatallowsaWebservertorunaprogramorscriptontheserverandsendtheoutputtoaWebbrowser.

cluster

Agroupthatiscreatedbasedoncertaincriteria.Forexample,ageneclustermayincludeasetofgeneswhosesimilarexpressionprofilesarefoundtobesimilaraccordingtocertaincriteria,oraclustermayrefertoagroupofclonesthatarerelatedtoeachotherbyhomology.

Cn3D

“Seein3-D”isastructureandsequencealignmentviewerforNCBIdatabases.Itallowsviewingof3-Dstructuresandsequence–structureorstructure–structurealignments.Cn3Dcanworkasahelperapplicationtothebrowserorasaclient–serverapplicationthatretrievesstructurerecordsfromtheMolecularModelingDatabase（MMDB,seebelow）directlyfromtheinternet.TheCn3Dhomepageprovidesaccesstoinformationonhowtoinstalltheprogram,atutorialtogetstarted,andacomprehensivehelpdocument.

codon

SequenceofthreenucleotidesinDNAormRNAthatspecifiesaparticularaminoacidduringproteinsynthesis;alsocalledatriplet.Ofthe64possiblecodons,3arestopcodons,whichdonotspecifyaminoacids.

COGs

ClustersofOrthologousGroups（ofproteins）weredelineatedbycomparingproteinsequencesfromcompletelysequencedgenomes.EachCOGconsistsofindividualproteinsorgroupsofparalogsfromatleastthreelineagesandthuscorrespondstoanancientconserveddomain.

consensussequence

ThenucleotidesoraminoacidsfoundmostcommonlyateachpositioninthesequencesofhomologousDNAs,RNAs,orproteins.

contig

Acontiguoussegmentofthegenomemadebyjoiningoverlappingclonesorsequences.Aclonecontigconsistsofagroupofcloned（copied）piecesofDNArepresentingoverlappingregionsofaparticularchromosome.Asequencecontigisanextendedsequencecreatedbymergingprimarysequencesthatoverlap.AcontigmapshowstheregionsofachromosomewherecontiguousDNAsegmentsoverlap.Contigmapsprovidetheabilitytostudyacompleteandoftenlargesegmentofthegenomebyexaminingaseriesofoverlappingclones,whichthenprovideanunbrokensuccessionofinformationaboutthatregion.

Coriell

CoriellInstituteofAgingCellRepository

CPU

CentralProcessingUnit.TheCPUisthecomputationalandcontrolunitofacomputer,thedevicethatinterpretsandexecutesinstructions.

CSS

CascadingStyleSheets.CSSspecifytheformattingdetailsthatcontrolthepresentationandlayoutofHTMLandXMLelements.CSScanbeusedfordescribingtheformattingbehaviorandtextdecorationofsimplystructuredXMLdocumentsbutcannotdisplaystructurethatvariesfromthestructureofthesourcedata.

Cubby

AtoolofEntrez,theCubbystoressearchstrategiesthatmaybeupdatedatanytime,storesLinkOutpreferencestospecifywhichLinkOutprovidershavetobedisplayedinPubMed,andchangesthedefaultdocumentdeliveryservice.

DCMS

DataCreationandMaintenanceSystem

DDBJ

DNADataBankofJapan

definitionline

AsequenceinFASTAforma