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Hence, only plots containing at least one of these host plant species at a minimum abundance (>5% cover in May 2006) were used for this study (Table S1).
For that reason, the abundance estimates using this method will always result in a minimum abundance.
Data utilized in the histogram was restricted to miR observed at a minimum abundance ratio level of 5 per thousand miR observed.
Nine automatically detected feature pairs (Table S-3) with a minimum abundance of 10 counts were selected for subsequent MS/MS experiments.
One limitation of this method is that it requires a minimum abundance and uptake rates of the target group in the sample (Teira et al., 2004).
Both the native and the U-C precursor ions had to exhibit a minimum abundance of 10 counts in at least three recorded scans for being selected for successive LC-HRMS/MS measurements and evaluation by FragExtract.
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Finally, the nine Sphingobium strains and enriched pathways were clustered heirarchially using Pearson correlation with 0.8% minimum abundance and a heat map was constructed in MeV4.9.0 [ 64].
A second way to identify the core genome would be to make protein clustering and a cut-off of abundance, this is shown in the column named "Core.Prot.Fam", using a threshold of 11 for the minimum abundance.
Before quantitation a second filtering step was performed to retain only those proteins with enough abundance (minimum abundance of 0.001) for a low-biased quantitation [ 90, 91].
Proceeding from the average abundance of an element in the crust, and the minimum abundance that can be profitably exploited under normal circumstances, a factor of enrichment necessary to produce an ore deposit can be derived (see Table).
Minia was compiled using the make k = 100 option to include higher k-mer sizes and run with a k-mer size of 31 and minimum abundance of 4. Mira (version 3.4.1.1) was run in accurate mode (job=denovo,genome,accurate,solexa SOLEXA SETTINGS GE:tismin=100 tismax=200) on a subset of 20 million reads randomly chosen from library 24 by a custom Python script.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com