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This cut-off was the most stringent parameter setting applicable and ensures that the datasets show no substantial sequence similarity.
Core promoter predictions for transcripts associated with protein-coding genes in microsynteny blocks were performed with McPromoter using the most stringent parameter values (Ohler 2006).
If we chose the most stringent parameter, we would expect that from our 1,135 microsatellite-containing sequences, 729 would be suitable for primer synthesis (46% of mean attrition rate on this step), and 365 would be polymorphic (50% mean attrition rate).
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In our experiments, primers were retrieved from the GETPrime database based on Ensembl release 50 with the most stringent parameters if available, or with the slightly less stringent design method 'DesignRelaxed'.
With the most stringent parameters (ontology coverage = 1, within-ontology agreement = 1, inter-ontology agreement = 1), 222 of them were defined automatically as part_of, 15 as is_a, all the others as broader_than.
To evaluate the accuracy of the L er-0 revised sequence, locus-specific reads were mapped to all three sequences (Col-0, L er-0 draft, and L er-0 revised) using the most stringent parameters (no gaps and no ambiguities were allowed).
These numbers and also the ratios between the respective sampling points remain constant even after applying the most stringent statistical parameters.
The forcelevel flag specifically reduced the stringency during the final contigs merge pass with 0 being most stringent and 10 least stringent, standard parameters using 0. When the forcelevel was relaxed slightly to 3, the percent coverage was nearly the same with only a slight drop in percent identity.
Parameters for the most stringent assembly (designated A1) included a 25 base match requirement for entry into the assembly, a 95% similarity requirement, a 50 base spacing for matching mers (tags used to accelerate assembly), a minimum of 50 bases per sequence, a gap penalty of 0.25, a gap length penalty of 0.5, and a maximum of 15 mismatched end bases.
These two parameters have a big impact on latency, the most stringent QoS requirement.
As clearly documented in the work of Kim et al., we used the most stringent EPP value as our study was focused on "strict divergent gene analysis parameter" [ 65].
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