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dc.contributor.authorWilson, Mandy L.
dc.contributor.authorCai, Yizhi
dc.contributor.authorHanlon, Regina
dc.contributor.authorTaylor, Samantha
dc.contributor.authorChevreux, Bastien
dc.contributor.authorSetubal, Joao C.
dc.contributor.authorTyler, Brett M.
dc.contributor.authorPeccoud, Jean
dc.date.accessioned2019-04-15T14:27:15Z
dc.date.available2019-04-15T14:27:15Z
dc.date.issued2013-01
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/10919/88963
dc.description.abstractGene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.en_US
dc.description.sponsorshipNational Science Foundation (NSF) [EF-0850100, DBI-1241328]; Agriculture and Food Research Initiative of the National Institute of Food and Agriculture of the USDA [2010-65110-20764]; NSF Award [DBI-1241328]; USDA [2010-65110-20764]
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCreative Commons Attribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectgene synthesis
dc.subjectgenome
dc.subjectbiology
dc.subjectbioinformatics
dc.subjectretrieval
dc.subjectalignment
dc.titleSequence verification of synthetic DNA by assembly of sequencing readsen_US
dc.typeArticle - Refereed
dc.description.notesNational Science Foundation (NSF) [EF-0850100, DBI-1241328 to J.P.]; Agriculture and Food Research Initiative of the National Institute of Food and Agriculture of the USDA [2010-65110-20764 to B. M. T.]. Funding for open access charge: NSF Award [DBI-1241328]; USDA [2010-65110-20764].
dc.title.serialNucleic Acids Research
dc.identifier.doihttps://doi.org/10.1093/nar/gks908
dc.identifier.volume41
dc.identifier.issue1
dc.type.dcmitypeText
dc.identifier.pmid23042248
dc.identifier.eissn1362-4962


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License: Creative Commons Attribution 4.0 International