Announcement

CodonUsageDatabaseisanextendedWWWversionofCUTG(CodonUsageTabulatedfromGenBank).ThefrequencyofcodonuseineachorganismismadesearchablethroughthisWorldWideWebsite.

CUTGwasoriginallydevelopedbyProf.ToshimichiIkemuraatLaboratoryofEvolutionaryGenetics,NationalInstituteofGenetics.

CodonUsageDatabaseisdevelopedandmainteinedbyYasukazuNakamuraatTheFirstLaboratoryforPlantGeneResearch,KazusaDNAResearchInstitute.

Datasource

NCBI-GenBankFlatFileRelease141.0[May112004].

Filespri(primatesequenceentries),rod(rodentsequenceentries),mam(othermammaliansequenceentries),vrt(othervertebratesequenceentries),inv(invertebratesequenceentries),pln(plantsequenceentries),bct(bacterialsequenceentries),vrl(viralsequenceentries)andphg(phagesequenceentries)wereused.

Filesforest(EST:expressedsequencetagsequenceentries)andpat(patentsequenceentries),rna(StructuralRNAsequenceentries),sts(STS:sequencetaggedsitesequenceentries),syn(syntheticandchimericsequenceentries)anduna(unanotatedsequenceentries)werenotused.

Allofthecompletesequencedproteincodinggenes(CDS"s)areused.Codonscontainingambiguousbasewereexcludedfromcount.

Dataamount

21,733organisms1,125,820completeproteincodinggenes(CDS"s)

Usage

Aqueryboxtosearchacodonusagetableforanorganism,ispresented.SearchcanbedonewithLatinnameoritssub-stringoforganism.Defaultsearchprocessiscasesensitive.Caseinsensitiveoptioncouldbeselected.Ambiguousquerywhichhitsover100organismsreturnsnoanswer.

Nameoforganism,shownintheanswerlistforqueryoralphabeticallist,isfollowedbynameofdivisionofGenBank[gbbct,gbinvetc.],colonandnumberofcompiledCDS.Likethis;

ArABIdopsisthaliana[gbpln]:23188

Ifyouselectalinkforanorganism,codonusagetablefortheorganismwillbeshown.Thetableshowsfrequency(perthousand)andcountforeachcodonasasumofallCDS"softheorganism.TablewhichincludeaminoacidsorwhichisformattedasGCGstyle(construction)arealsoshownwhenonegeneticcodesystemisselected.BacktranslationprogramwhichisusefultodesignPCRprimersinproteincodingareaalsoavailable(construction).

Selectingthelink"CodonusageofeachCDS"underthetable,youwillbrowseordownloadallcodonusagetablesofCDS"sintheorganism.TheformatoftableisCUTGstyle(Seebelowlinkfor"CODEN_LABEL"fileinCUTG).

CUTG:CodonUsageTabulatedfromGenBank

CodonusagetablesforallCDS"sforeachGenBankdivision(pri,rod,mam,vrt,inv,pln,bct,vrlandphg)willbedownloadedfrom"FTPlinksforCUTGfiles"linkintoppage.

AdocumentREADMEcontainsthelatestinformationonthedatabaseinplaintextformat.CODON_LABELandSPSUM_LABELfilesshowfileformats.

Acknowledgment

WewishtothankDr.Ugawa*atTheDNAInformationandStockCenter,NationalInstituteofAgroBIOLOGicalResourcesforhelpinconstructinganddistributingthedatabasefrom1996to1999.

[*PresentaddressofDr.UgawaisEnvironmentalEducationCenter,MiyagiUniversityofEducation]

ThisworkwassuportedbyaGrant-in-AidforScientificResearch(Grant-in-AidforPublicationofScientificResearchResults)fromJapanSocietyforthePromotionofScience.

Pleasecite

CodonusagetabulatedfromtheinternationalDNAsequencedatabases:statusfortheyear2000.Nakamura,Y.,Gojobori,T.andIkemura,T.(2000)Nucl.AcidsRes.28,292.

(NARDatabaseIssuepage)

Thisarticlegivesreferencestoearlierpapers.

QUERYBoxforsearchwithLatinnameoforganism

Alphabeticallistsofallorganisms

ABCDEFGHIJKLMNOPQRSTUVWXYZChloroplastMitochondrionOthers(intialsarenotcapital)

---

CUTG:CodonUsageTabulatedfromGenBank(ftpdistribution)

---

AdditionalServiceCountcodonprogram:compilationasequenceintoacodonusagetable