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A plot where a number of random probes corresponding to the number of probes resulting by setting stringency conditions is shown in Additional file 8F.
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An E-value of 10-6 wasetet as stringency threshold.
The increase in usable reads allowed us to set high stringency conditions for mapping (97.5% identity).
This method is based on the PolyPhred program and uses the 'rank' argument to set the stringency.
This value was calculated for each frame of each image, and we set a stringency that the starting image should have a value with no greater than 10% deviation (0.9 < (A − C /(B − C) > 1.1).
On real biological data, we furthermore observe that the proportion of duplicated genes and therefore of missed orthologs is considerable even in bacteria and archaea (5 50% missed orthologs depending on the data set and stringency of the analysis).
Whether this difference is the result of the new implementation of Scansite3, potentially setting new underlying stringency thresholds, or due to the addition of a minimum stringency level is not clear.
Data were analyzed in the "Functional Annotation Clustering" tool using the "High" classification stringency setting for Molecular Function (MF) and Biological Process (BP) Gene Ontology (GO) terms.
We used the highest stringency setting to detect significantly enriched annotation clusters with P < 0.05 and FDR < 0.25.
The best-performing classifier, Decision Tree (DT), identified at the more relaxed 'Neutral' stringency setting almost 80% of the known MAE genes with 20% false positive rate.
We then evaluated potential off-targets for all the candidates by setting "Maximum" for "stringency" and "NGG and NAG" for "PAM".
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com