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In genomics, transcriptomics, population genetics, and metagenomics, these are widespread fundamental tasks solved by different computational methodologies (Table 2), though based on similar strategies (Fig. 2), mainly ab initio approaches or similarity-based ones.
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Different computational methodologies have been developed to quantify the uncertain response of a relatively simple aeroelastic system in limit-cycle oscillation, subject to parametric variability.
We generated and analysed gene co-expression networks with different computational methodologies: Clustering with Overlapping Neighborhood Expansion (ClusterONE) [ 37], inference of gene regression networks with model trees (RegNet) [ 38], and the Weighted Gene Co-Expression NetWGCNA(WGCNalgorithmthm [ 39].
Since the two problems are usually addressed by different computational techniques, they are often investigated separately.
The parameter values of these simulation models have been estimated to be consistent with the data by some computational methodologies.
These octapeptides were characterized by using different computational procedures.
Therefore, we scanned the whole genome sequence of B. subtilis by using different computational approaches.
DOMINE contains DDIs inferred from PDB entries and those by eight different computational approaches.
The apparent discrepancy between the two genomic contigs may reflect an artifact introduced by using computational methodology because of the high sequence identity among the different LCRs or other aspects of the complex genome organization in the region.
All together, these results confirm that the re-engineered TRNs proposed by our computational methodology mimic the transcriptomic response observed under real viral infections by altering a smaller and different set of targets than those observed during the transcriptomic characterization of real infections.
Our results indicate the importance of CTC heterogeneity for their detection by different analytical methodologies.
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