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We elected to not treat cases of embedded overlapping genes in this study.
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Zhu et al. design a diversified discrimination score based on the log ratio which can reduce the overlap between selected features by considering the embedding overlaps in the graphs [46].
In strain DM4, genes dcmR and dcmA are embedded within several overlapping IS elements ([79], Table 3 and see below, Fig. 6).
The resulting porous GN@CuInS2/C nanofibers were 107 ± 24 nm in diameter, and graphene nanosheets anchored with chalcopyrite CuInS2 nanocrystals 7 12 nm in diameter were overlapped and embedded in the carbon matrix, aligning along the fiber axial direction.
Of these probesets, three were co-incidentally positioned to overlap the embedded miRNAs within the primary transcript (let-7b:1440357_at; miR-425:1459927_at; miR-214: 1427298_at).
The majority of the same-strand overlaps are embedded forms, whereas most different-strand overlaps are not embedded and in the convergent transcription orientation.
Table 2 shows that the majority of same-strand overlaps are embedded forms, accounting for ~89% and ~79% of overlapping genes in the human and mouse genomes, respectively.
We can notice that some embedding areas may overlap because of the proximity of the corresponding feature points.
Moreover, sequences resembling this consensus target function optimally when embedded in a cluster of overlapping similar sequences [ 33].
And on Flickr, Faramarz Hashemi has collected the set of #iranelection photos embedded below (some of them overlap with the ones on Twitter).
For the majority of same-strand overlaps, overlap regions account for 90 100% of the shorter gene but less than 10% of the longer gene, consistent with the observation that the majority of same-strand overlaps are embedded forms (Table 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com