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Frequency rankings of particular culture-specific contigs are shown in Supplementary Tables S4 S12.
The frequency rankings of the AAUAAA motif among all 4096 possible hexanucleotide motifs for each species are listed in Additional file 2. A-rich motifs of AAUAAA and AAAAUA showed certain predominance in the potato late blight pathogen Phytophthora infestans (Table 2).
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Although the non-parametric rank product method does not make any assumptions about the data distribution, it can provide frequency ranking scores at each data point and is thus a robust tool for creating ranking lists.
For Alzheimer's disease, we analyzed the outcome of the frequency based ranking method and calculated the precision, F-score and rank for different recall ranges (10%, 30%, and 50% recall) and determined the maximal F-score (see Table 3).
Yet, there were differences in frequency and ranking order, particularly across countries, as reported in table 4 and illustrated in box 2. "Antiretroviral medication is quite hard to take.
Although frequency-based ranking leads to higher gene enrichment slope between the ranks 300 and 1500, we observe a stronger enrichment at low ranking positions using relative entropy-based ranking.
It is given by χ 2 = ∑ i k ! r i 2, where r i = O i - E i E i is the Pearson residual, and O i, E i are the observed and expected frequencies of ranking i, respectively.
The mean frequency of the rankings of the set of measures was calculated to yield the final set of measures.
As a consequence the availability of three rankings (frequency, incidence, and PI) renders the decision on the most important field for prevention difficult if the rankings differ.
Traditional screening methods have used observed crash frequency or severity ranking criteria and statistical modelling approaches, despite the fact that crash-based methods are reactive.
It is also possible that using this methodology some large proteins may have scored higher than other smaller proteins due to their containing likely more trypsin cleavage sites and consequently generating more associated peptides that may have skewed the ranking frequency in their favor.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com