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Activated Stat proteins form dimers, enter the nucleus, and bind to specific DNA sequences to affect gene transcription [31].
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A more general model could allow changes to the protein sequence to affect both the protein's function and the cost of expression.
Another important consideration for chemical labeling in living cells is the potential of the probe or targeting sequence to affect the cellular system via toxicity or more complicated interactions, which have to be ruled out by suitable controls and improved labeling protocols.
This could be the result of incomplete genomic sequencing (though to affect the same protein in two species barley and rice seems unlikely), or that in both cases the mRNA annotated as MVP, was a contaminant.
The occurrence of differential hybridization due to sequence diversity in probe regions may be thought specific for short-oligomer arrays: sequence differences in short sequences are supposed to affect hybridization more than in longer sequences.
For example, the redesign may avoid sequences most prone to deletion (e.g., by eliminating repeats) but also introduce various types of extra sequences to potentially affect regulation.
In coding sequences, accumulation of uptake sequences is expected to affect the outcome of natural selection on protein function.
LNA modifications were predicted (1) to decrease the level of mismatch discrimination of VAL-A and VAL-B sequences, (2) not to affect discrimination of VAL-C and VAL-D sequences, and (3) to enhance mismatch discrimination of VAL-E, VAL-F, and VAL-G sequences.
Only three sequence variations presumed to affect the coding sequence of SLC26A5 in humans have been reported to date.
Prior to this report, only three other DNA sequence variations expected to affect the coding sequence of human SLC26A5 were known: splice site variant IVS2-2A>G upstream of the ATG start codon [15]; missense variant p.I67V [17]; and, missense variant p.R150Q [18].
These sequences are used to affect the stochastic nature of the algorithm as shown above in Eq. (4).
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