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Information about sampling procedure, filter preparation, extraction of nucleic acids, sequencing strategy, sequence quality check and taxonomic assignment (on the phylum level) of the samples can be found in Logares et al. (2014) [ 18].
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However, not all sequences could be confidently assigned taxonomy to the genus level; therefore we denote these sequences by appending the tag unclassified to the end of their taxonomic assignment (one of phylum, class, order, or family levels).
Nevertheless, no significant differences were apparent between the two treatment treatments analysis on the phylum level or the order level.
In addition EST projects have provided an abundance of sequence information on the phylum [ 15].
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For a class level of novelty, all BLAST matches to the same class were removed, and assignments were made at the phylum level.
The assignment of Thermobaculum terrenum to the phylum Chloroflexi in 2011 [49].
One of the best examples of the wrong assignment using NCBI-NR is the node Oryza (21 reads mapped to an unknown protein [ Oryza sativa Japonica Group]), all of which should be assigned to Lachnospiraceae in the phylum Firmicutes.
However, in order to relate the selection specifically to a response vector, like the phylum assignment, we need a selection based on a supervised learning method.
Phylum-level species assignment showed that species belonging to the phylum Firmicutes were most largely affected by both probiotics, and all species belonging to the phylum Bacteroidetes were affected only by Lactobacillus probiotics (Table 1).
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