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Relaxing the stringency (decreasing the cut-off score from the maximum of 100) progressively increased this number; using a cut-off score of ≥1, there were 4482, which represents an increase of 30% over the total number of Wormbase predicted clone-target pairs.
An analysis of the ICN is shown in Figure 2. Because the number of α-links remains constant and, typically, β-links are added to the network, the total number of links in the network increases on average with respect to increasing clustering stringency (decreasing ω) for all ϕ (Fig. 2a).
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Then, the stringency was decreased from 1e−45 to 1e−15 with the 'Ends to Ends' auto merge function.
Then, the stringency was decreased at nine successively lower cutoff from 1e-60 to 1e-15.
Increasing values of stringency will decrease the rate of wrong allocations but will also increase the rate of non-allocated individuals.
Next, the "Ends to Ends" auto merge function was used with default settings and the stringency was decreased from 1e-40 to 1e-15.
Signal loss was initially evaluated at 50%% and the stringency was decreased in increments of 10%% until reaching a 20%% loss of signal.
Reduced stringency by decreased hybridisation temperature maximized the overall number and intensity of signals, but this was accompanied with 30% increase of unspecific hybridisation signals.
In that case the stringency was decreased from 1e-40 tonlyly 1e-25 becausingletonsonlyonly had to match on one side.
It has been demonstrated previously (Suardi et al, 2008; Conti et al, 2009; Mufarrij et al, 2010) that increases in stringency can decrease the rates of adverse pathological features but will also substantially decrease the number of men suitable for AS.
Then each candidate is tested using different methods with decreasing stringency to assign them to the most probable known effector gene (see Methods section).
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