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With medium stringency, no significant cluster was presented.
We therefore searched for homologs of the TRGs in the clam symbionts and SUP05 with a lower BSR of up to 0.25, but even with this reduced stringency, no hits were found (see 'Materials and methods').
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Considering each of these models covering a range of stringencies, no association of EGFR copy number status with overall survival, PFS and best overall response was found.
Vector trimming was performed manually and contig assembly was performed using the DNAStar software (low stringency settings, no vector trimming).
It is interesting to note that all trGTPases were retrieved at E-value 1e-10, and searches at lower stringency yielded no additional ones (Table 1).
An examination of mutual information between residues in CydX using the Mutual Information Server to Infer Co-evolution (MISTIC) web server [ 31] found that, even at the lowest stringency, absolutely no mutual information was detected between the N-terminal residues and those in the C-terminus.
Another factor affecting the outcome of the analysis is the bioinformatic analysis pipeline [ 22] and its stringency level, since no standard operating procedure is currently available.
Data were normalized using Block Lowess method and then analyzed at two levels of stringency (one with no data excluded; the second, data excluded when "Quality less than 1; Confidence less than 0.4; PON Ch1 or Ch2 less than 0.6").
Since this was a manageable list, and probably related to the direct effect of the treatment, no further stringency filters were applied thus removing experimenter involvement.
Even at lower stringency, sYG2 still had no female alignments so we decided to include it.
In both cases high stringencies were used, with no mismatch permitted.
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