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While this problem is intractable in general, we identify several tractable classes of preferred repairs that are useful in practice.
We analyze the complexity of the notion, and we extend an algorithm for evaluating DL-programs to compute repair answer sets, under optional selection of preferred repairs that satisfy additional constraints.
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However, NHEJ seems to be the preferred repair mechanism in this organism [36], [37].
In a related green alga, C. reinhardtii, NHEJ is the preferred repair mechanism [37] although both NHEJ and HR could be used [36].
It is not a preferred repair mechanism in the related green alga C. reinhardtii [37], however, it is the main repair mechanism in other unicellular organisms like yeast [70] and in mouse embryos [71].
For example, in a G1 cell, NHEJ is likely the preferred repair choice.
gBGC, which prefers repairing DNA mismatches with GC bases in hetero-duplexed recombination intermediates (Marais 2003; Duret and Galtier 2009), is ubiquitous in eukaryotes (Pessia et al. 2012; Glémin et al. 2014) and prokaryotes (Lassalle et al. 2015).
We do not know the mechanism underlying this similarity, but these sites might share preferred DNA-repair mechanisms with a resulting similar bias for specific use of nucleotides and oligonucleotide "words" [ 25].
Open repair of descending and thoracoabdominal aneurysms is preferred because endovascular repair may result in late failure due to continued dilation of fixation zone or persistent perfusion of the false lumen.
Yeast prefer to repair DSBs by HR (Manolis et al., 2001).
ALKBH2 prefers to repair damage in duplex DNA over ssDNA, however.
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Justyna Jupowicz-Kozak
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