Sentence examples for using the ribosomal database from inspiring English sources

Taxonomy was assigned using the Ribosomal Database Project (RDP) classifier (Cole et al. 2014).

Sequenced DNA was compared using the Ribosomal Database Project (RDP and GenBank-National Center for Biotechnology InformationNCBICBI) database, and sequence similarities above 99% were considered identified for species the level and above 98% for the genus level.

Taxonomy was assigned to sequences longer than 100 bp using the Ribosomal Database Project Classifier tool [19].

Sequences longer then 100bp were taxonomically annotated to the level of genus using the Ribosomal Database Project Classifier tool [30] with a bootstrap cutoff of 50%.

The sequenced cDNA libraries (after one cycle of mRNA enrichment) contained 80.6% ribosomal RNA sequences, and taxonomic assignments were successfully made for 4.0% of these sequences (25,398 total sequences) using the Ribosomal Database Project classification algorithm [30] (Figure 1B).

Unaligned, sequences in the equilibrated dataset were given taxonomic assignments at a bootstrap confidence range of ≥95% using the Ribosomal Database Project's Naïve Bayesian Classifier tool (RDP classifier) [25], [35].

Then we used the ribosomal database project (RDP) classifier (Cole et al., 2009) to infer the taxonomy for each sequence.

A prior study used the Ribosomal Database Project classifier (v2.2) with the default 032010 training set and taxonomy to annotate these sequences [ 49].

We used the Ribosomal Database Project (RDP) classifier 2.2 [ 23] against the Greengenes database (2012 release, available at http://greengenes.lbl.gov/) [ 20] using the same thresholds we used for MG-RAST.

The sensitivity and the specificity of the Bacteroidetes, Firmicutes and M. smithii systems were assessed in silico using the ribosomal RDP-II database [17].

Phylogenetic analysis Alignments of the 16S rRNA gene were made using sequences downloaded from the Ribosomal database project II (RDP II; Cole et al. 2005), after searching for nearest neighbors using the sequence match tool.