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The MAR databases: development and implementation of databases specific for marine metagenomics
Klemetsen; Raknes; Fu; Agafonov; Balasundaram; Tartari; Robertsen; Willassen (2018). The MAR databases: development and implementation of databases specific for marine metagenomics. Nucleic Acids Res. 46(D1): D692-D699. https://dx.doi.org/10.1093/nar/gkx1036
In: Nucleic Acids Research. Information Retrieval: London. ISSN 0305-1048; e-ISSN 1362-4962
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| Auteurs | | Top |
- Klemetsen, T.
- Raknes, I.A.
- Fu, J.
- Agafonov, A.
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- Balasundaram, S.V.
- Tartari, G.
- Robertsen, E.
- Willassen, N.P.
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| Abstract |
We introduce the marine databases; MarRef, MarDBand MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. |
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