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There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address.
These restorations and annotations are necessary for constructing datasets that takes the DNA into consideration, making them real non-redundant "complex structures", not just non-redundant in terms of proteins.
There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task.
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We also constructed datasets in which the sources were not perfectly phase locked.
We demonstrate the advantages of the two-layer encoders qualitatively on artificially constructed datasets as well as commonly used benchmark datasets.
Using the described selection criteria, the disorder indices of the proteins in all six independently constructed datasets were calculated.
> Only a subset of the domains in the constructed datasets have an experimentally solved structure available.
We constructed datasets composed of 7,342 nucleotide sites from nine concatenated genes.
We also found that the model was able to successfully infer evolutionary dynamics in artificially constructed datasets.
We constructed datasets exclusively composed of sequences captured several times (see methods) which should be essentially free from artefactual mutations [ 36].
Similar to previous studies with constructed datasets [ 5, 6, 17, 18, 21], our data show global compression most extreme at very high and low gene expression values.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com