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Assigning TF pairs with similar biological function to similar binding sequences may have additional functional advantages.
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Some of the sequences might be false positives with no TFBSs, whereas other sequences may have binding sites for other cofactors.
TE sequences may have interesting properties, non-coding sequences containing fortuitous ORFs, binding sites for regulation by proteins, or just useful chemico-physical properties.
These binding sites may have low sequence specificities, but their binding affinities can be complemented by high structure specificities.
Alternatively we cannot rule out that sequence divergence in these samples at primer binding sites may have prevented amplification.
As with the failed attempt to amplify nuDNA from the two relatively recent specimens, an explanation may simply be that sequence divergence in the problematic samples at the primer binding sites may have prevented amplification.
These EMSAs suggested that Cas8′ in isolation can recognize PAM sequence and may have structural preference for binding stably to branched DNA or R-loops compared with duplex DNA.
Current availability of extensive genome sequence data, allows one to identify less numerous, nevertheless biological important organic phosphate-binding domains that may have previous eluded detection.
Based on sequence similarity, CG5555 may have zinc ion binding and ubiquitin-protein ligase activities.
The lack of apparent nuclear protein binding to the DNA sequence around SNP-638 may have resulted from inappropriate reaction conditions in detecting specific binding in the present study.
Each of these sequences encodes at least one potential transcription factor binding site suggesting these regions may have regulatory function.
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