GenoLIB: a database of biological parts derived from a library of common plasmid features

dc.contributor.authorAdames, Neil R.en
dc.contributor.authorWilson, Mandy L.en
dc.contributor.authorFang, Gangen
dc.contributor.authorLux, Matthew W.en
dc.contributor.authorGlick, Benjamin S.en
dc.contributor.authorPeccoud, Jeanen
dc.date.accessioned2019-04-11T18:07:54Zen
dc.date.available2019-04-11T18:07:54Zen
dc.date.issued2015-05-26en
dc.description.abstractSynthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of similar to 2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects.en
dc.description.notesNSF Awards 1241328; Natural Science Foundation of China (No. 61173113 to G.F.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Funding for open access charge: NSF Awards 1241328.en
dc.description.sponsorshipNSF [1241328]; Natural Science Foundation of China [61173113]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkv272en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue10en
dc.identifier.pmid25925571en
dc.identifier.urihttp://hdl.handle.net/10919/88892en
dc.identifier.volume43en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectsynthetic biologyen
dc.subject72-base-pair repeaten
dc.subjectdna-replicationen
dc.subjectcodon biasen
dc.subjectsequenceen
dc.subjectstandarden
dc.subjectdesignen
dc.subjectexpressionen
dc.subjectvectorsen
dc.subjectoriginen
dc.titleGenoLIB: a database of biological parts derived from a library of common plasmid featuresen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
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