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To maintain the accuracy in contig assembly, further reduction in stringency to merge more contigs was not pursued in this study.
A subsequent reduction in stringency (1e-5) allowed a further 8% of contigs to be assigned a putative function (thus, 76% of the O. marina contigs could not be identified, Table 1).
The high threshold represents the most conservative annotation approach (with the least false-positives), followed by a gradual reduction in stringency, including medium-high, medium-low, and low thresholds.
After using the DQer to break up contigs consisting of more than 10% questionable clones, a consecutive reduction in stringency at 1e-5 for each End-End and Single-End merge using the "clone plus markers (CPM)" function at a tolerance of 3 was performed to reassemble contigs.
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Such variants could be identified by a modest reduction in the stringency levels and verified by Sanger sequencing.
Whilst this is not an exact science, care was taken where possible to follow a similar selection strategy for each hapten class (increasing stringency though reduction in antigen concentration and the swapping of protein conjugates to minimize the selection of carrier protein specific clones etc).
Increasing the z-score filter resulted in increasing the stringency, and a concomitant reduction in the number of protein domain pairs selected (Table 1).
ICAO estimated the cost of this increase in stringency to be approximately $5 billion.
Offshore jurisdictions vary in stringency.
Male and female examiners showed no overall difference in stringency.
These methods vary in stringency and have different potential biases.
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