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.
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).
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).
Summarizing all simulations, one observation can be made: The amount of total assignments of reads to taxa correlates with the read length.
Therefore, according to eq 3, the FDR is calculated by doubling the number of decoy matches divided by the number of total assignments.
For a given level in the taxonomy tree (e.g., genus), we define precision as the fraction of correct assignments over the total number of assignments, and sensitivity as the ratio between the number of correct assignments and the number of objects to be classified.
Of these, 1,958 had associated GO terms encompassing 15,160 total assignments.
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.
