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dc.contributor.authorDelmans, Men
dc.contributor.authorPollak, Bernardoen
dc.contributor.authorHaseloff, Jimen
dc.date.accessioned2017-04-19T11:16:42Z
dc.date.available2017-04-19T11:16:42Z
dc.date.issued2017-01-27en
dc.identifier.issn0032-0781
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/263690
dc.description.abstract$\textit{Marchantia polymorpha}$ is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, $\textit{M. polymorpha}$ is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for $\textit{M. polymorpha}$ genetic parts where each gene is a standalone functional unit. MarpoDB is a database of $\textit{M. polymorpha}$ genes and genetic parts, which is tailored to become an integral tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non-redundant $\textit{Viridiplantae}$ BLAST annotations; BLAST querying to $\textit{M. polymorpha}$ genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a minimalistic, intuitive and interactive user interface for gene models and sequence exploration. Furthermore, we have implemented user input to encourage feedback, collaboration and exchange between the MarpoDB community. MarpoDB source-code is released on GitHub to promote development of computational tools for synthetic biology.
dc.description.sponsorshipThis work was supported by the Chilean Comisión Nacional de Investigación Científica y Tecnológica (CONICYT) [Becas Chile and Cambridge Trust joint Scholarship to B.P.]; the Biotechnology and Biological Sciences Research Council and Engineering and Physical Sciences Research Council Synthetic Biology Research Centre supported by the Research Councils’ Synthetic Biology for Growth Programme [OpenPlant grant No. BB/L014130/1 to J.H.]; and University of Cambridge BBSRC DTP programme [M.D.]
dc.languageengen
dc.language.isoenen
dc.publisherOxford University Press
dc.rightsAttribution 4.0 Internationalen
dc.rightsAttribution 4.0 Internationalen
dc.rightsAttribution 4.0 Internationalen
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectgenetic partsen
dc.subject$\textit{Marchantia polymorpha}$en
dc.subjectgenetic databasesen
dc.subjectopen source databaseen
dc.subjectplant synthetic biologyen
dc.titleMarpoDB: An Open Registry for $\textit{Marchantia Polymorpha}$ Genetic Partsen
dc.typeArticle
prism.issueIdentifier1en
prism.numbere5en
prism.publicationDate2017en
prism.publicationNamePlant & Cell Physiologyen
prism.volume58en
dc.identifier.doi10.17863/CAM.9052
dcterms.dateAccepted2016-11-03en
rioxxterms.versionofrecord10.1093/pcp/pcw201en
rioxxterms.versionVoRen
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/en
rioxxterms.licenseref.startdate2017-01-27en
dc.contributor.orcidPollak, Bernardo [0000-0003-2329-7401]
dc.contributor.orcidHaseloff, Jim [0000-0003-4793-8058]
dc.identifier.eissn1471-9053
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idBBSRC (BB/L014130/1)
cam.orpheus.successThu Jan 30 12:54:00 GMT 2020 - The item has an open VoR version.*
rioxxterms.freetoread.startdate2100-01-01


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International