The first is the total assignment cost, and the second is the total weighted resource consumption.
First, restraints are automatically divided into three confidence classes according to a total assignment probability score19: highly confident (HI) (probability >70%), confident (MED) (probability >45%) and least confident (LOW) (probability <45%).
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).
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.
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.
Therefore, according to eq 3, the FDR is calculated by doubling the number of decoy matches divided by the number of 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.
Individual categories that represented less than 1.0% of total assignments included Protein fate (14, 0.85%), Protein activity regulation, (18, 0.82%), Cell cycle and DNA processing (10, 0.7%), Transposable elements, viral and plasmid proteins (38, 0.34%), Interaction with the environment (36, 0.25%), Cell fate (40, 0.23%) and Cell type differentiation (43, 0.11%).
