Generalized DNA Barcode Design Based on Hamming Codes 英文参考文献.docVIP

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Generalized DNA Barcode Design Based on Hamming Codes 英文参考文献.doc

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Generalized DNA Barcode Design Based on Hamming Codes 英文参考文献

GeneralizedDNABarcodeDesignBasedonHamming Codes LeonidV.Bystrykh* Section Stem Cell Biology, European Research Institute on the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands Abstract The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hammingcode-basedsequencesaresuggestedandillustrated.HammingbarcodescanbeemployedforDNAtagdesigns inmanydifferentwayswhilepreservingminimaldistanceanderror-correctingproperties.Inaddition,Hammingbarcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoptionofimprovedHammingbarcodesisencouragedinmultiplexparallelsequencingapplications. Citation:BystrykhLV(2012)GeneralizedDNABarcodeDesignBasedonHammingCodes.PLoSONE7(5):e36852.doi:10.1371/journal.pone.0036852 Editor:Jo-AnnL.Stanton,UniversityofOtago,NewZealand ReceivedNovember10,2011;AcceptedApril13,2012;PublishedMay17,2012 Copyright:?2012LeonidV.Bystrykh.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:TheworkispartiallysupportedbySeventhFrameworkProgrammeoftheEuropeanUnion,SP3-People,HEM_IDITNgrant(MarieCuriegrantforinitial training). The funders