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This experimental setup likely represents the highest possible editing efficiency, as a similar approach in C. elegans reported highly efficient genome editing (Paix et al. 2015).
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EEEP identifies discordance between a test tree and a reference tree and infers, when possible, edits paths which reconcile observed instances of discordance.
The topological comparison of phylogenetic trees is inherently difficult, as the number of possible edit paths (where one rearranges the branches of one tree to match another's) increases rapidly with the number of differences between trees.
Without resorting to heuristics and its inherent approximations, and without constraining the types of possible edits (apart from those that are biologically impossible: LGT with one's ancestor), we are therefore limited to comparing trees that are relatively similar.
Figure 6 shows the mean edit path length recovered for each size class of protein trees, compared to the maximum possible edit path length (= n - 3) and the mean edit path length recovered from comparisons between 500 pairs of random trees.
This competition between exogenous and endogenous sequence complicates the analysis of possible gene editing outcomes make it difficult to predict the consequence of gene editing.
We also detected possible RNA editing events in nAChR genes.
It is possible that editing might restore presently unrecognized coding sequences.
In addition, a possible RNA editing signal similar to that found in the P gene of other paramyxoviruses is present.
Possible RNA editing was also found in three transcript variants of the B. mori α6 gene [ 18].
For endogenous gene-tagging applications, we thought it would be best to have the smallest footprint possible after editing, but still wanted to benefit from our selection scheme.
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CEO of Professional Science Editing for Scientists @ prosciediting.com