The phrase "a set of duplications" is correct and usable in written English.
It can be used when referring to multiple instances or copies of something that are identical or very similar.
Example: "In the analysis, we found a set of duplications in the data that needed to be addressed to ensure accuracy."
Alternatives: "a collection of duplicates" or "a group of copies".
Given a set of duplication blocks 𝒟, the maximum parsimony evolutionary history is the DAG G = (𝒟, E) that minimizes f(G) = ∑ Y ∈?? d(P G (Y), Y).
Here, we formalize the problem of computing a segmental duplication evolutionary history for a set of duplication blocks in the human genome with respect to either a parsimony or likelihood criterion.
We represent evolutionary relationships between a set of duplication blocks as a directed acyclic graph (DAG), and we formalize the evolutionary reconstruction problem as an optimization over the space of DAGs.
Here we propose a model that is in agreement with the Nishida's idea and predicts that the extant biosynthetic routes might have emerged after a set of duplication events involving the genes of the ancestral common pathway.
Given a set of duplication blocks 𝒟, the maximum likelihood evolutionary history is the DAG G = (𝒟, E) that maximizes the likelihood: where Z P G XX )(k ) and Q k ) P G (Y ) are the partition function and restricted partition functions, respectively.
The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes).
Benchmarking on reference-free metagenome datasets would have resulted in a set of duplicate clusters and an expected duplication rate but would give no indication of the accuracy of each method for duplicate detection.
Here, we present a novel formulation of the problem of computing an evolutionary history for a set of segmental duplications that are organized in duplication blocks.
A duplication history is a sequence of duplicate events that first builds up a set of seed duplication blocks by duplicating and aggregating duplicons from their ancestral loci and then successively constructs the remaining duplication blocks by duplicating substrings of previously constructed blocks.
We use a simulated annealing heuristic to solve the problem for a set of segmental duplications in the human genome in both parsimony and likelihood settings.
