Exact(60)
However, some sequences (e.g., CAM, SS, and MR) contained complex dynamic background sequences.
In Eigen's original proposal, the fitness landscape consists of a single peak along with other background sequences.
Consequently, background depletion and virome enrichment techniques are usually needed for clinical samples where viral load is much lower than background sequences.
In these kinds of dynamic background sequences, Park's method (in CAM, SS, and MR) and Li's method (in MR) performed slightly better than the proposed method.
The proper number of background sequences of each of the CG-content bins is sampled.
Three types of background sequences were prepared: random, core promoter and conserved promoter.
To develop a conserved promoter background, sequences with conservation scores higher than 75% for every gene were obtained and concatenated.
The comparison process between foreground and background sequences is the same as U-CGIs vs. M-CGIs.
Employing the human IPI database for background sequences, 7 significant motif patterns could be identified, covering over 53% of our dataset (Fig. 2A B).
The background sequences in the validation are also from M-CGIs as the methylation-prone data in the original datasets are too insufficient.
Then, by sampling data from the CGIs randomly, we constructed 10 groups of foreground sequences (promoter related CGIs) and background sequences (non-promoter related CGIs) with the same sample size and composition as U-CGIs and M-CGIs respectively, i.e. 304 foreground sequences (297 promoter-CGIs, 7 non-promoter-CGIs) and 210 background sequences (79 promoter-CGIs, 131 non-promoter-CGIs).
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