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Average nucleotide identity (ANI) was calculated as defined before (Konstantinidis and Tiedje 2005), using a minimum cut off of 50% identity and 70% of the length of the query gene.
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Mannan testing for the diagnosis of Candida infections was reported in two studies, each using a minimum cut-off of 0.5 ng/ml [ 56, 79].
As a minimum cut off for group comparisons, and 0.9 for individual comparisons.
An RSAT score of 4.5 was used as a minimum cut-off value in this analysis because this is the lowest score obtained for a bona fide ZRE found in the EKI1 promoter [ 21].
First, the sequences were filtered using a minimum quality cut off value of 40.
Is there a minimum cut-off?
A minimum cut-off for intensity and particle size was established.
All reads were assembled with a minimum cut-off similarity of 97% to remove pyrosequencing errors.
Consequently, our filtering was set to a minimum cut-off of 10 X CCS coverage depth.
Preliminary filtering of identified peptides was performed using a minimum cross-correlation cut-off (Xcorr) of either 1.9, 2.2, or 3.75 for 1+, 2+, or 3+ charge states, respectively, for fully tryptic (peptides that contained either an arginine or lysine at the site of cleavage), partially tryptic, and non-tryptic peptides.
All ESTs were then clustered by the Contig Express module in the Vector NTI package using a minimum overlap of 50 bp, an identity of 0.9 and a cut off score of 20.
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