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Afterwards the composed datasets are coded as XRFF files.
For each of the randomly composed datasets, the numbers of conjoint pathways were computed.
The false-positive error rate was determined by screening 1000 times, randomly composed datasets of various sample sizes (50, 200 and 1000 promoters) for various motifs and calculating the probability that a given motif is termed enriched by mistake.
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Therefore, we designed a randomization algorithm for the Motif Mapper software [ 37] which enabled statistical evaluation of motif enrichment in a specific promoter dataset compared to a randomly composed dataset.
In fact, the environment-specific datasets were the datasets which compose the multi-condition (combined) datasets, for example the multi-condition (combined) '5s.20u' datasets were composed by environment-specific '5s.5u' datasets of four environments.
We tested our method on a simulation dataset, a real dataset composed of several known genomes, and a real metagenome NGS short reads dataset.
The dataset is composed by three sub-datasets: (i) the Telecommunications Activity dataset providing the activity of Trentino, showing all the mentioned telecommunication events which took place within this area.
At the end, DS AMKL sample pool 'A' included 43 datasets, while non-DS AMKL sample pool 'B' was composed of 45 datasets.
For training samples, we randomly selected five positive datasets and five negative datasets each composed of 7500 Human sequences, and five positive datasets and five negative datasets each composed of 5000 Drosophila sequences.
The FAMeS artificial datasets (http://fames.jgi-psf.org/description.html), are mock metagenomic community datasets composed of random reads from 113 isolate microbial genomes.
For this reason, a benchmark composed of 24 datasets, from 60 to 1000 customers, has also been designed.
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