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dc.contributor.authorDanks, Gemma Barbara
dc.contributor.authorCampsteijn, Coen
dc.contributor.authorParida, Mruyunjaya
dc.contributor.authorButcher, Stephen
dc.contributor.authorDoddapaneni, Harsha
dc.contributor.authorFu, Bolei
dc.contributor.authorPetrin, Raul
dc.contributor.authorMetpally, Raghu
dc.contributor.authorLenhard, Boris
dc.contributor.authorWincker, Patrick
dc.contributor.authorChourrout, Daniel
dc.contributor.authorThompson, Eric
dc.contributor.authorManak, J Robert
dc.date.accessioned2016-06-02T10:37:36Z
dc.date.available2016-06-02T10:37:36Z
dc.date.issued2013-11-26
dc.PublishedNucleic Acids Research 2013, 41(D1):D845-D853eng
dc.identifier.issn1362-4962en_US
dc.identifier.urihttp://hdl.handle.net/1956/12051
dc.description.abstractWe report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO (http://www.geneontology.org) and InterPro (http://www.ebi.ac.uk/interpro/) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide download- able gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.en_US
dc.language.isoengeng
dc.publisherOxford University Press (OUP)en_US
dc.rightsAttribution CC BY-NC 3.0eng
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/eng
dc.titleOikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioicaen_US
dc.typePeer reviewed
dc.typeJournal article
dc.date.updated2016-04-07T09:20:31Z
dc.description.versionpublishedVersionen_US
dc.rights.holderCopyright The Author(s) 2012en_US
dc.identifier.doihttps://doi.org/10.1093/nar/gks1159
dc.identifier.cristin1027598
dc.subject.nsiVDP::Matematikk og naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474
dc.subject.nsiVDP::Mathematics and natural scienses: 400::Basic biosciences: 470::Genetics and genomics: 474
dc.subject.nsiVDP::Matematikk og Naturvitenskap: 400en_US


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Attribution CC BY-NC 3.0
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