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Searches of the GenBank database were conducted by using BLAST [ 40]. 16S rRNA sequences of representative homologous species were retrieved from GenBank to generate the phylogenetic tree (1,000 bootstrap replicates) using the maximum composite likelihood method and the neighbour-joining method in the MEGA5 program [ 41].
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A similarity search of the contigs against the National Center for Biotechnology Information (NCBI) nr database was conducted by BLASTX algorithm (Altschul et al., 1990) with an E-value cutoff of 1.0E-5.
The consent process for participation in the recruitment database is conducted by the patient's clinical team, most commonly by the patient's care coordinator (or, if not, by another member of the patient's care team).
The record linkage between CCHS and the administrative databases was conducted by Statistics Canada.
Database analyses were conducted by SC and JM.
Authors had full access to the database, and the statistical analyses were conducted by an academic team: Bio statistics Unit, Lille University Hospital, Lille, France, which worked in full independence from MSD. EA has been a consultant to Astellas, Alexion, Cubist, Gilead and MSD, and has benefited from grants to his research unit from Gilead and Pfizer.
All searches were conducted by using database SwissProt and NCBInr like MASCOT and only those peptides were reported as significant for which E value was statistically significant (E < 0.05).
Two replication studies using different UK PCDs reported closely corresponding results using different database sources; 15 17 however, these replications were conducted by research groups instrumental in the creation and maintenance of the comparator PCD and hence, lacked independence.
Signaling pathways were conducted by using KEGG database.
GO annotations were conducted by searching against the Nr database using Blast2GO (E-value of 1E-6) [ 31].
Prospective collected database was conducted from December 2014 to April 2015.
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