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We were able to reproduce the information in the published papers that was provided on these assignments in most cases (Table 4 and the Appendix of Coble et al., 2010).
The Optimal Assignment kernel is in most cases the best choice (an example is presented in Figure 1), because it shows comparably good results with each AD formulation and leads to very reliable rankings regardless of how the AD threshold is chosen.
In this case only few errors occur and the class assignment will be unequivocal in most cases.
False and missing orthology assignments could be attributed in most cases to missing or only incomplete gene predictions.
In most cases assignment to TLR families was straightforward.
Annotation of a genome involves assignment of functions to proteins in most cases on the basis of sequence similarity.
While in some cases the taxonomic assignment based on NR was the same as the one obtained using an appropriate method, in most cases the assignment to was to a taxon that is probably incorrect.
Assignment of unclassified proteins to structural superfamiles is also undertaken and in most cases substantiates assignments made using sequence similarity.
During the preliminary identification process, all specimens were identified to the generic level using only external morphological criteria, but their species-level assignment were not possible or correct in most cases.
In most cases, the assignment to specific macroregion/s was based on the observed geographic distribution in our sample set (supplemented with data from literature for previously known branches).
The results show that the time delay derived from flow assignment carried out by this approach is, in most cases, better than those determined using conventional routing heuristics.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com