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Subsite binding energies were predicted with r2 = 0.502 correlation coefficient, while bond cleavage frequency prediction resulted in r2 = 0.538.
Our results indicate that pressure solution cleavage frequency exhibits a spatial distribution that depends on the position within the fold.
We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting "neutral" elements.
We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting neutral RSs.
It was transformed from a 6-bp recognition site enzyme to one of combined 2.9-bp specificity, thus radically increasing cleavage frequency from 4096 bp to 57.7 bp.
The cleavage frequency in a wild-type strain is too low to obtain a library comparable to that of the H4S47C strain, which requires that two cleavages are sufficiently close to generate <500-bp fragments for paired-end sequencing.
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Calculations for training set resulted in good correlation in case of subsite binding energies (r2 = 0.827 0.929) and bond cleavage frequencies (r2 = 0.727 0.835).
Cleavage frequencies for samples taken at 3, 4 and 6 hours after induction were virtually identical (Fig. 2), suggesting that Pho4 reached binding equilibrium at UASp1 between 2 and 3 hours after induction.
To determine cleavage frequencies, isolated DNA was digested with restriction enzymes to release a 3 kb fragment encompassing the PHO5 gene, fractionated by gel electrophoresis, blotted and hybridized with a radiolabeled DNA probe that recognizes sequences upstream of the PHO5 promoter (Fig. 2).
In an initial consideration of the primary sequence, we used the MEROPS tool to correlate cleavage frequencies experimentally associated with the three residues N-terminal and four residues C-terminal to the cleavage sites in the various ubiquitin dimers.
For both enzymes, the cleavage frequency of the glycosidic bond of maltooligosaccharides was the highest at the second bond from the reducing end.
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