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Protocols

INSDC specifications

Information


Unique identifier OMICS_01653
Name INSDC
Alternative name International Nucleotide Sequence Database Collaboration
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/International_Nucleotide_Sequence_Database_Collaboration

Maintainer


  • person_outline Ilene Karsch-Mizrachi

Publication for International Nucleotide Sequence Database Collaboration

INSDC citations

 (152)
library_books

A thin ice layer segregates two distinct fungal communities in Antarctic brines from Tarn Flat (Northern Victoria Land)

2018
Sci Rep
PMCID: 5919928
PMID: 29700429
DOI: 10.1038/s41598-018-25079-3

[…] carded. Assembled reads were analyzed via Qiime v.1.8 software package. Sequences were checked for chimeras with the Chimera VSEARCH. Next, fungal sequences were taxonomically annotated using UNITE + INSDC dataset June 2017 release. Operational taxonomic units (OTUs) table was generated using demultiplexed sequences at 97% similarity and singletons were removed. All sequences have been submitted t […]

call_split

Phylogeography of hydrothermal vent stalked barnacles: a new species fills a gap in the Indian Ocean ‘dispersal corridor’ hypothesis

2018
R Soc Open Sci
PMCID: 5936951
PMID: 29765686
DOI: 10.1098/rsos.172408
call_split See protocol

[…] (Biomatters Limited) and registered to DNA Data Bank of Japan, with accession numbers LC350007–LC350015.The sequences obtained were aligned with eolepadid sequences available in the databases of the International Nucleotide Sequence Database Collaboration, using Clustal X included in MEGA v. 6.06 []. A total of 123 sequences from seven eolepadid taxa were used (4--45 individuals per taxa), with o […]

library_books

The efficacy of 16S ribosomal DNA sequencing in the diagnosis of bacteria from blood, bone and synovial fluid samples of children with musculoskeletal infections

2018
PMCID: 5902756
PMID: 29707061
DOI: 10.1302/1863-2548.12.170049

[…] uencing results were analyzed with Geneious bioinformatics software (Biomatters, New Zealand) and compared with the National Center for Biotechnology Information world database for bacterial species (International Nucleotide Sequence Database Collaboration).Standard laboratory procedures were performed in parallel for each sample and pathogen and served as the reference index in the present study. […]

library_books

A world without bacterial meningitis: how genomic epidemiology can inform vaccination strategy

2018
F1000Res
PMCID: 5871810
PMID: 29636909
DOI: 10.12688/f1000research.13793.1

[…] l Isolate Genome Sequence Database (BIGSdb) platform (PubMLST.org), which stores assembled and annotated genome data from the meningococcus and pneumococcus , . This supplements resources such as the International Nucleotide Sequence Database Collaboration, which is composed of the National Center for Biotechnology Information, the European Nucleotide Archive and the DNA Databank of Japan. Global […]

library_books

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome

2018
Sci Rep
PMCID: 5807544
PMID: 29426844
DOI: 10.1038/s41598-018-20783-6

[…] to the total number reads observed in the data set) greater than 0.01%. Ecological functions were attributed based on the metadata associated with the BLAST closest matches recovered in the UNITE and INSDC (www.insdc.org) databases and by cross-referencing the literature (details provided in supplementary information and in Supplementary Tables  and ). […]

call_split

A new species of the genus Pseudocrangonyx (Crustacea, Amphipoda, Pseudocrangonyctidae) from South Korea

2018
Zookeys
PMCID: 5904333
PMID: 29674860
DOI: 10.3897/zookeys.735.21697
call_split See protocol

[…] 28S rRNA, histone H3, COI and 16S rRNA from three Korean Pseudocrangonyx specimens were newly obtained in this study, and deposited into the International Nucleotide Sequence Database Collaboration (INSDC) through the DNA Data Bank of Japan (Table ).The OTU set for phylogenetic analyses was almost identical to that used in the previous phylogenetic analyses in with the DNA sequences of P. elegan […]

Citations

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INSDC institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; DDBJ Center, National Institute for Genetics, Mishima, Japan; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
INSDC funding source(s)
Supported by the NCBI thanks to the Intramural Research Program of the National Institutes of Health; National Library of Medicine; European Nucleotide Archive by the European Molecular Biology Laboratory, the Horizon 2020 Programme of the European Commission and the Biotechnology and Biological Sciences Research Council; the Ministry of Education, Culture, Sports, Science and Technology, the Research Organization of Information and Systems, Japan.

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