CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data 英文参考文献.docVIP

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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data 英文参考文献.doc

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CDinFusion – Submission-Ready, On-Line Integration of Sequence and Contextual Data 英文参考文献

CDinFusion–Submission-Ready,On-LineIntegrationof SequenceandContextualData WolfgangHankeln1,2,NormaJohannaWendel1,3,JanGerken1,2,JostWaldmann1,PierLuigiButtigieg1,2, IvayloKostadinov1,2,RenzoKottmann1,PelinYilmaz1,2,FrankOliverGlo¨ckner1,2 * 1MaxPlanckInstituteforMarineMicrobiology,Bremen,Germany,2JacobsUniversitygGmbH,Bremen,Germany,3FachhochschuleBingen,BingenamRhein,Germany Abstract Stateoftheart(DNA)sequencingmethodsappliedin‘‘Omics’’studiesgrantinsightintothe‘blueprints’oforganismsfrom alldomainsoflife.Sequencingiscarriedoutaroundtheglobeandthedataissubmittedtothepublicrepositoriesofthe International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted oftengetslost,becauseexperimentaldata,aswellasinformationabouttheenvironmentarerarelysubmittedalongwith thesequencedata.Ifthesecontextualormetadataaremissing,keyopportunitiesofcomparisonandanalysisacrossstudies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promoteschecklistsandstandardstobetterdescribeoursequencedatacollectionandtopromotethecapturing,exchange andintegration ofsequencedata withcontextualdata. Inarecentcommunityeffortthe GSChas developeda series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific communitytosignificantlyenhancethequalityandquantityofcontextualdatainthepublicsequencedatarepositories, specializedsoftwaretoolsareneeded.InthisworkwepresentCDinFusion,aweb-basedtooltointegratecontextualand sequence data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU PublicLicense3.ApublicinstallationishostedandmaintainedattheMaxPlanckInstituteforMarineMicrobiologyathttp:// /cdinfusion. The tool may also be installed locally using the open source code available at http://code. /p/cdinfusion. Citation: Hankeln W, Wendel NJ, Gerken J, Waldmann J, Buttigieg PL, et al. (201