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Summarizing all simulations, one observation can be made: The amount of total assignments of reads to taxa correlates with the read length.
Of these, 1,958 had associated GO terms encompassing 15,160 total assignments.
Therefore, according to eq 3, the FDR is calculated by doubling the number of decoy matches divided by the number of total assignments.
The actual FDR that is observed, on the other hand, is the number of incorrect assignments divided by the total assignments.
We estimated the prevalence of the codes by calculating the percentages of positive assignments compared to the total assignments issued by all of the evaluators.
For the gill, 5,156 of the 6,352 sequences in the library mapped to 2,278 unique putative homologues, with 2,109 having associated GO terms encompassing 18,258 total assignments.
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The first is the total assignment cost, and the second is the total weighted resource consumption.
The objective of the BIP is to minimize the total assignment costs and is, thus, following a min-cost strategy.
Results of the CAZyme Analysis Tool (CAT) revealed that the most encoded CAZyme domain included the Glycoside Hydrolase (GH) family (~50 % of total assignment), followed by the Carbohydrate Binding Modules (CBM) (~30 %), Glycosyl Transferases (GT) (~15 %) and a rest of the proportion (~5 %) comprising Pectate Lyases (PL) and Auxiliary Activities (AA) (Additional file 5: Figure S4).
In such cases, each assignment was counted in the statistic Total Subsystem Assignments in Table S8 in SI (so that the gene was counted more than once).
Finally, this paper tries to design the proper assignment policy that the total locomotive assignment cost is minimized by making a tradeoff between travel time, travel distance, and waiting time, and considering the different degrees of priority (by maximizing the satisfactions of trains in service).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com