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The phenotype associated with the master sequence is catalytic and has two dangling ends.
A chromosomal master sequence is the collection of physically distinct whole and fragmented chromosomes in the cell.
Moreover, the master sequence is a far outlier with respect to the neutrality distribution for random units of replication (fig. 5, first pane).
The self-replication rate of the master sequence is rather high, due to its long dangling ends and the C– G-based strategy for complex formation.
Figure 3 clearly shows that after a few hundred generations, much more variants survive, the master sequence is below 14% of the total population and still the populations are changing drastically.
The master sequence is also nonmodular: The fraction of units of replication obtained when mutating only the dangling ends of the catalytic strand is only slightly higher than the neutrality of the whole sequence (λ tails = 0.11 ).
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In contrast, a GYSVd1 master sequence was not identified because the sequenced variants of this viroid differed from each other at least in one position (Fig. S2).
The master sequence was confirmed by the database to contain the appropriate, biologically relevant HIV genes, and several drug resistant mutations were also identified.
This is in analogy to certain quasispecies analysis, in which sequences with a similar Hamming distance towards the master sequence are lumped together [ 51].
Copies of the master sequence are more or less clustered and separated from parasites, which (as expected) are closer to the regions with empty space.
In figure 4, bottom row, the relative fractions of functional classes arising as mutants of the master sequence are compared with those of optimized sequences and random ones (as before).
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