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In-paralogs and out-paralogs are defined based on the relative order of duplication and speciation events.
The precise order of duplication events is however unclear.
Although the number of duplication steps that separates the different enzymes is clear, the order of duplication is not.
In our dataset this is also the most frequent relationship observed for the human chromosomes, possibly reflecting the order of duplication events.
The relatively high and low P-value indicate that the SOPH approach is able to reconstruct, in a largely independent way, the relative order of duplication events.
We would like to use all these histories to compute probabilities for particular events (e.g. interaction events or an order of duplication events) to have occurred.
Similar(47)
These values may reflect the order of each duplication event, and herein we propose models to explain the order of duplications.
Further, both methods assume the relative ordering of duplication events is known even between events in unrelated homology groups.
Here, we introduce a combinatorial framework for representing histories of network evolution that can encode gene duplication, gene loss, interaction gain and interaction loss at arbitrary times and does not assume a known total ordering of duplication events.
From Figure 3 the order of gene duplication events can be traced, with an MPO-EPO-LPO MRCA arising from a gene duplication with extant TPO; then a further duplication event that gave rise to, (i) the MPO-EPO MRCA, and (ii), the lineage leading to extant LPO; and the final and most recent duplication of the MPO-EPO MRCA into extant MPO and EPO clades.
In order to further clarify the evolutionary order of the duplication events in each group, we defined the best hit for each duplicated gene as its direct parental gene (Materials and Methods).
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