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3. Consider Alignment.
First, it may be interesting to consider alignment of weighted PPI networks with weights representing, for instance, experimental evidence of interaction existence.
A suggested way to solve this problem is to consider alignment as a random variable, a strategy developed into the statistical alignment procedure [ 49, 50].
The former consider alignment of stem cell images whereas the latter is concerned with registration of retinal images, which differs from our problem in that it requires registration transformations of another type (quadric transformations).
The challenge is to convince organizations and their staff to consider alignment efforts as a valuable dimension of research projects, instead of extra burden, because of its influence on project contributions and on trust in and legitimacy of the organization in a broader sense.
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We argue here that next-generation phylogenomics should consider alignment-free methods as an alternative – but not the only one.
They specifically consider alignments without explicit capture of insertions or deletions.
GSNAP takes as input the file containing reference and non-reference alternate alleles to equally consider alignments to both alleles.
We did not consider alignments in which the Conservation score with Cons was less than 20% as these alignments are of very poor quality.
Usually, we consider alignments A together with structures S of A and T of B, forming the triple (S, T, A ).
After that, the final tool path is modified by considering alignment error, tool radius error and squareness error.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com