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After that, all the aligned sequences were clustered and we only retained clusters that had exactly one representative member from each subgenome and located on similar position of homeologous group.
Orthologous groups with exactly one representative protein from each of the 34 input strains were considered to be part of the E. faecium core genome.
The clustering output was further filtered for conserved orthologous genes as a representative from each species - that is, having exactly one representative in the cluster for each of the species.
Therefore, only homeologous gene loci that had exactly one representative member from each subgenome (referred to as homeologous triplets, 4565 × 3 = 13,695 genes) (Additional file 12 and 17) were selected for further analysis.
This choice maximized the number of protein families with exactly one representative in each of the five genomes (480 single copy protein families) and corresponds to the threshold selected by Lerat, Daubin and Moran [ 26] and Lerat et al. [ 9].
A first tree was constructed based on the average distances between species in the 480 single copy protein families (i.e. the protein families that contain exactly one representative in each of the five genomes considered) (Fig. 2b).
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This resulted in a set of 5,075 orthologous groups, of which 1,512 were considered to belong to the core genome as they contained exactly one protein representative from each of the 34 input strains.
But that may be exactly the point: one representative of a large multinational consumer goods company was delighted to think how consumer-led innovation could erase the normally bureaucratic process her company takes: "consumer-led processes are better than filling out endless forms".
Cluster II contains exactly one protein each from the species with a representative in cluster Ib.
"We are a little bit surprised by what's going on exactly, because we have not been informed about a vote," one representative told the General Assembly.
Figure 18A shows a representative image of the whole array, where each of the five adjacent electrode pairs was connected by exactly one nanotube.
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