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Peter Godfrey-Smith has also since introduced a notion of a reproducer that is more broadly inclusive, in that it relaxes the material overlap requirement and focuses on an understanding of "who came from whom, and roughly where one begins and another ends".
The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology.
However, short partial adapter sequences, which often occur at the ends of reads, are inherently unable to meet this minimum overlap requirement and therefore are not detectable.
Sixth, sequences were collapsed based on gapped alignments, again allowing any extent of overlap meeting the minimum overlap requirement of that assembly job.
Even a loose BLAST overlap requirement has the effect that it anchors the hit to the right family, thereby greatly reducing the number of conflicts and number of false family assignments at these levels.
For the medium confidence annotation we lower the BLAST overlap requirement to a BLAST E-value cutoff of 0.1 and for the low confidence annotation we need no overlap in the BLAST comparison.
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The built-in scaling of assembly overlap requirements by PRICE to reflect local coverage was intended to address these biases.
Approximately 75% of re-annotated gene models could be assigned a Gene Ontology term [ 16].> -wrap-foot> Four different minimum overlap requirements (expressed as a fraction of the Chiifu reference gene model) used to compare two gene models at both gene level and exon level.
Although not qualitatively different from the fifth collapse step (described in the paragraph to follow), which allowed sequences to overlap only partially, the full-overlap requirement provided numerous algorithmic advantages over the equivalent operation allowing overlaps.
It is important to note that this is not a watering down of standards, but simply the elimination of overlapping requirements.
Results will inform minimum requirements, such as the type and thickness of barrier material, apron design and extent of the overlap required for optimal protection.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com