The private sector, on the other hand, is plagued by a remarkably inefficient landscape of a million mom-and-pop shops served by complex layers of re-sellers.
Accuracy of both the nesting structure and the time layers of re-annotation was calculated as the proportion of RE ANNOTATE predictions in agreement with manually curated annotation.
RE ANNOTATE's predictions in the three layers of re-annotation achieved excellent accuracy relative to manual annotation, with results shown in Table 2 (see Implementation for calculation).
In this study, the evolution of stress fields and structural phase composition have been studied using Raman spectroscopy pre- and post-transition in the oxide layer of re-crystallised ZIRLO and recrystallised zircaloy-4 (Zr-4) after corrosion exposure in a static autoclave.
This first layer of re-annotation consequently contains the chromosomal distribution of repetitive element integration events.
Accuracy of the defragmentation layer of re-annotation was assessed by its sensitivity and specificity at the element level.
Building upon the insertion models of the Defragmentation layer of re-annotation, RE ANNOTATE resolves any nested structures among the repetitive elements identified.
This layer of re-annotation implicitly contains the age distribution of 'complete' LTR-elements, and bounds on the ages of other kinds of sequences that may be found overlapping LTR-elements.
Although the analyses above focused on the annotation of LTR-elements, they also validate the automated re-annotation of other kinds of repetitive elements and were chosen for two main reasons: i) Models of LTR-elements in the first (Defragmentation) layer of re-annotation are more complex than models of other repeats.
If a 'complete' LTR-element is found in a nested cluster of repetitive elements, the previous Nesting Structure layer of re-annotation allows the placement of i) an upper bound on the age of any elements nested within, and ii) a lower bound on the age of any elements nesting, the LTR-element.
