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Protocols

PR2 Database specifications

Information


Unique identifier OMICS_03164
Name PR2 Database
Alternative name Protist Ribosomal reference database
Restrictions to use None
Maintained Yes

Maintainers


  • person_outline Laure Guillou
  • person_outline Daniel Vaulot

Publication for Protist Ribosomal reference database

PR2 Database citations

 (20)
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Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro eukaryotes from a suspected homicide to estimate the post mortem interval

2018
Sci Rep
PMCID: 5758714
PMID: 29311698
DOI: 10.1038/s41598-017-18179-z
call_split See protocol

[…] removed when the average phred score of a 50 nucleotides window was below 20. Chimera were identified and discarded using the program Uchime (v. 7.0.1090) by comparing sequences among them and to the PR2 database. The sequences were then clustered into Operational Taxonomic Units (OTUs) using the software Swarm (v. 1.2.12) with the default parameters. The OTUs were finally taxonomically assigned b […]

library_books

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

2017
PLoS One
PMCID: 5667844
PMID: 29095959
DOI: 10.1371/journal.pone.0187636

[…] and clustered at 97% identity threshold. Reads were then mapped against the representative set of sequences generated in the clustering step and taxonomy was assigned against the Protist Ribosomal 2 (PR2) database [] at 97% threshold, using the UCLUST assigner implemented in QIIME []. In order to reduce the potential introduction of artefact sequences [], OTUs represented by fewer than 10 sequence […]

library_books

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters

2017
PMCID: 5739019
PMID: 29027996
DOI: 10.1038/ismej.2017.166

[…] with an average length of 398 bp. These sequences were clustered into 6900 OTUs. Finally, sequences were classified using the knn algorithm implemented in mothur and the BLASTN search method with the PR2 database (cut-off of 80%) (). The raw sequence data have been deposited in the NCBI Sequence Read Archive under the BioProject: PRJNA316490. […]

library_books

Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the ‘abundant’ and ‘intermediate’ biospheres

2017
Sci Rep
PMCID: 5573402
PMID: 28842665
DOI: 10.1038/s41598-017-10308-y

[…] ring was done using Uparse at the 97% similarity cutoff . Generation of OTU tables and taxonomy assignment of each OTU were done with QIIME using the reference taxonomic database of ciliates from the Protist Ribosomal Reference database (PR2). Sequences were normalized by randomly resampling 14,825 reads per sample (the lowest number of sequences recovered for 97 samples), which minimized bias ass […]

call_split

Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

2017
Front Microbiol
PMCID: 5469884
PMID: 28659910
DOI: 10.3389/fmicb.2017.01121
call_split See protocol

[…] e also removed. Reads were then clustered into Operational Taxonomic Units (OTUs) at 95% sequence similarity using UPARSE (Edgar, ). The taxonomy assignment of OTUs was achieved by UCLUST against the PR2 database to detect and remove taxa that are not affiliated with eukaryotes (e.g., Bacteria, Archaea, and plastidial sequences) (de Vargas et al., ). The OTUs affiliated with Metazoa or Unassigned […]

library_books

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

2017
Front Microbiol
PMCID: 5411419
PMID: 28512451
DOI: 10.3389/fmicb.2017.00738

[…] ained in this study did not overlap, a specifically tailored workflow was used to process the raw 18S rRNA gene amplicon sequencing data. For the classification step and the taxonomic assignment, the PR2 database (Guillou et al., ) was used according to Hu et al. (). […]

Citations

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PR2 Database institution(s)
CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Roscoff, France

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