Sequence verification of synthetic DNA by assembly of sequencing reads

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dc.contributor.authorWilson, Mandy L.en
dc.contributor.authorCai, Yizhien
dc.contributor.authorHanlon, Reginaen
dc.contributor.authorTaylor, Samanthaen
dc.contributor.authorChevreux, Bastienen
dc.contributor.authorSetubal, Joao C.en
dc.contributor.authorTyler, Brett M.en
dc.contributor.authorPeccoud, Jeanen
dc.date.accessioned2019-04-15T14:27:15Zen
dc.date.available2019-04-15T14:27:15Zen
dc.date.issued2013-01en
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
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].en
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]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gks908en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue1en
dc.identifier.pmid23042248en
dc.identifier.urihttp://hdl.handle.net/10919/88963en
dc.identifier.volume41en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectgene synthesisen
dc.subjectgenomeen
dc.subjectbiologyen
dc.subjectbioinformaticsen
dc.subjectretrievalen
dc.subjectalignmenten
dc.titleSequence verification of synthetic DNA by assembly of sequencing readsen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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