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Being aware of those alternatives, we decided to use a reference set of true signals that was created prospectively during the real-life process of validating SDRs generated by the SSD system.
However, this method does not use a reference set of sequences during the evaluation of significance, making it the most easily affected of these three approaches by PWM-to-PWM similarities (as measured by GC content differences).
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To evaluate the signal detection quality, we used a reference set of true signals.
Using a reference set comprising all A. thaliana proteins with at least one phosphorylation site, no over- or underrepresented categories could be identified.
Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set.
This comparison was done using a reference set consisting of protein coding sequences available in GenBank that are putatively expressed in the bloodstream stage.
(v) A graphical representation can be made of the weight of each codon along a multiple protein alignment that has been translated to a DNA alignment using a unique reference set for all the sequences of the alignment or using a reference set for each sequence.
As a second strategy, a hidden Markov model (HMM) for each of the RNA-binding domains was constructed using a reference set of genes annotated from the "text" based search using hmmbuild in package HMMER version 3.0 [ 106].
A strength of our study is that we used a reference set, or gold standard, of articles that could be identified in a following step through a newly developed search strategy and filters.
Researchers have also proposed integrating heterogeneous data sources with supervised approaches to predict co-complex protein pairs (protein pairs that belong to the same complex), using a reference set of training complexes.
In case of GWA meta-analyses, each individual cohort performs its own imputation using a reference set (e.g. HapMap or 1000 Genome) and statistical analysis prior to the combination of results.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com