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Protocols

cpnDB specifications

Information


Unique identifier OMICS_01511
Name cpnDB
Restrictions to use None
Maintained Yes

Publication for cpnDB

cpnDB citations

 (11)
library_books

Reproducible protocols for metagenomic analysis of human faecal phageomes

2018
Microbiome
PMCID: 5892011
PMID: 29631623
DOI: 10.1186/s40168-018-0446-z

[…] on were estimated by classifying reads with SortMeRNA v2.0 [] against the SILVA database [] to assess 16S rRNA abundance and by aligning reads using bowtie2 (--very-sensitive preset mode) against the cpnDB [] to assess abundance of cpn60 gene. A selection of total faecal DNA metagenomic samples (sample IDs SRS012902, SRS013158, SRS013215, SRS014613, SRS014923, SRS015854, SRS016095, SRS016753, SRS0 […]

library_books

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non pregnant women

2017
Sci Rep
PMCID: 5569030
PMID: 28835692
DOI: 10.1038/s41598-017-07790-9

[…] ma.sourceforge.net) with Trinity as the assembly tool. Assembled OTU were labeled according to their nearest reference sequence determined by watered-Blast comparison to the cpn60 reference database, cpnDB_nr (downloaded from http://www.cpndb.ca‚ÄČ ). cpnDB_nr is a subset of the cpnDB database that includes a non-redundant collection of sequences representing all species in cpnDB, with a preference […]

library_books

Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences

2016
Int J Syst Evol Microbiol
PMCID: 5244502
PMID: 27667728
DOI: 10.1099/ijsem.0.001501

[…] One hundred and thirty-three cpn60 UT sequences were retrieved from the cpnDB () and NCBI nucleotide sequence databases. Fifty-five cpn60 UT sequences from phytoplasma, along with three sequences belonging to Acholeplasmas, three from Mycoplasmas, one from Clostridia, 19 […]

call_split

Comparison of Methods to Identify Pathogens and Associated Virulence Functional Genes in Biosolids from Two Different Wastewater Treatment Facilities in Canada

2016
PLoS One
PMCID: 4835084
PMID: 27089040
DOI: 10.1371/journal.pone.0153554
call_split See protocol

[…] downstream analyses. The cpn60 sequences were subjected to the same initial process using the tools available in the RDP pyrosequencing pipeline. The four sequence datasets were then compared to the cpnDB (http://cpndb.cbr.nrc.ca/) using blastn []. Blast results were analyzed using MEGAN to place the sequences in the NCBI taxonomy using a lowest common ancestor algorithm [].For shotgun metagenomi […]

library_books

Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada, Belgium and Kenya

2016
PLoS One
PMCID: 4709144
PMID: 26751374
DOI: 10.1371/journal.pone.0146510

[…] ded in this study was determined by Sanger sequencing as previously described []. Phylogenetic comparison was carried out including cpn60 universal target sequences extracted from the cpn60 database, cpnDB (www.cpndb.ca) [], as well as all available whole genome sequences in the Integrated Microbial Genomes Expert Review (IMG/ER) database []. Full-length 16S rRNA gene sequences were available for […]

library_books

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60 Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types

2015
PLoS One
PMCID: 4534464
PMID: 26266808
DOI: 10.1371/journal.pone.0135620

[…] as the assembly tool []. Assembled OTU (> 150 bp) were identified and labeled according to their nearest reference sequence determined by watered-Blast comparison [] to the cpn60 reference database, cpnDB_nr_vag (downloaded on September 18, 2014 from http://www.cpndb.ca, []). OTU having less than 55% identity to any reference sequence were considered to be non-cpn60 sequences and removed from the […]

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cpnDB institution(s)
National Research Council Plant Biotechnology Institute, Saskatoon, SK, Canada

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