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We extracted clusters from these surrogate matrices and selected the cluster with the largest summary t value for each surrogate.
We extracted clusters from these surrogate matrices and selected the cluster with the largest summary t value (RS Asamevs. RSAdiffer) for each surrogate.
We should mention that finding clusters from these subspaces by running DBSCAN or any other density based clustering algorithm will take relatively very less time.
By combining these two groups, we obtained 29,882 predicted protein clusters from these small clusters.
The results presented here, together with information derived from our previous studies [20], [21], are suggestive of a mechanism where podosomes proliferate and transform from individual dynamic structures, that can nucleate sporadic adhesions, to 2-dimensional arrays ("clusters"); from these much more highly dynamic rings are formed, which eventually stabilize.
We have noticed that the reported edge clusters from these small hybrid graphs are not frequent.
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We find that 181,505, and 184 of these clusters from the respective comparisons contain more than one protein from either organism.
In addition, an intuitional view was provided to understand their major molecular functions by six clusters from the clustering of these genes with themes in synaptic transmission, signal transduction, metabolic process, and apoptosis.
At this stage, we could not tease apart the three scenarios and we therefore decided to exclude these clusters from the data set.
After selecting C1 and C2 the procedure FINDORDERING removes these clusters from the collection and replaces them with their union C' = C1 ∪ C2.
A phylogenetic analysis of the complete gene cluster from these three species and from Brassica oleracea confirmed its rapid evolution resulting from gene duplication and gene loss events, numerous amino acid substitutions, and insertions/deletions in the coding sequence.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com