For example, the case of strain 17573 that showed the lowest P-value (6.93×10−67 in RDP, 2.52×10−17 in Geneconv, 2.76×10−27 in Bootscan, 1.34×10−25 in MaxChi, 7.33×10−29 in Chimaera and 2.96×10−19 in SiScan) among those of all predicted recombination events.
Moreover, the advent of many PCR-based approaches, as well as sequencing projects, has led to the explosion of 16S rRNA gene sequences now available in major specialized sequence repositories, such as Greengenes (4), SILVA (5) and RDP (6).
OTUs were given taxonomic assignments in QIIME61 version 1.7.0 using RDP classifier62 and Greengenes database release 13_5.
Within the framework of a project financed by the Abruzzo Region with funding from the 2007-2013 RDP, the methodology of Carbon Footprint (OIV 2013.
More than 72% of the urine sequences best-matched only 25 RDP sequences.
The sequence coverage of the forward and reverse primers was tested using the Probe Match feature at the Ribosomal Database Project release 10 (RDP 10; http://rdp.cme.msu.edu; [27]).
In addition, the following statistical tests for detecting recombination were used: GENECONV [ 46], RDP, and MaxChi [ 47] analyses in the RDP version 2 b08 program package [ 48].
Intragenic recombination was detected using Phi (Bruen et al. 2006), RDP (Martin and Rybicki 2000), and OnePop (Hao 2010).
Recombination Detection Program v3.44 (RDP) [ 33] and Simplot v3.5.1 [ 34] software were initially used to scan for recombination signals under default settings.
These databases include several rDNA datasets too, e.g. GREENGENES [ 143], RDP II [ 144], and European 16 S RNA [ 145], among other information sources.
