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For each window of specified length, the script calculates the total number of degeneracies in the sense and antisense DNA strand across the entire gene.
These reflect structural expectations, e.g. the five most discouraged 4mers all feature two-residue helices (none of which is possible in the real world) and QEZ and ZEQ feature among the most discouraged 3mers due to the necessity of maintaining the parallel/anti-parallel nature of a strand across a beta-bulge.
METAL tries to resolve or flag common problems that result from an inconsistent choice of allele labels or genomic strand across studies, or the presence of invalid P-values or test statistics at a subset of markers (due to numerical errors).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com