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Analysis of the three sequence regions described above (I homeodomain only, II full-length, III extended homeodomain) was performed using more stringent settings.
These alignments were re-scored with RNAz using more stringent settings.
Although the opposite happens in AGC (serine) and UCG (serine), they disappear under more stringent settings.
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Searchs were performed under the default settings, except that the Expectation Value (E) was decreased from 10 to the more stringent setting of 1e-5.
The following parameters were changed from default settings: -fastMap, -minIdentity = 99, -maxIntron = 5, and -minScore = 30 (87% of the CENH3 reads and 82% of the control reads could be aligned with the much more stringent setting -minScore = 300).
A combination of binning and more stringent program settings reduced the degree of map expansion to a negligible level (2.8 ± 2.3%), but had the side effect of breaking up linkage groups (Table 2).
Criteria for the usefulness of a "new" discovery should be more stringent in clinical settings [ 31].
These required criteria are much more stringent than typical default settings.
If the settings are more stringent, more sites will be assigned as no-calls by the filter and the overall call rate will be reduced, but calls made will be more reliable.
Most settings were not varied throughout the test runs except for the tracking threshold of PG that was set more stringent than its default value, unless indicated otherwise.
Drug specifications for use in resource-limited settings may be more stringent than for developed countries as issues such as treatment durability, feasibility of manufacturing fixed-dose combination, and the possibility of being used without biological or virological monitoring are even more important.
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