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The pairwise similarity measure between sequences must map sequences to an evolutionary feature space ruled by the modification of sequences in terms of insertions, deletions and substitutions.
For our discussion, noise is any modification of sequences that destroys the true signal or that produces false signals.
One limitation of the CRISPR system is the potential for off-target modifications, i.e., the modification of sequences similar to the intended target sequence [ 13, 36].
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Although X-chromosome inactivation and silencing are usually considered to be mainly related to epigenetic effect [ 49], some studies also suggested that the change of gene regulation caused by epigenetic modification of sequence variation might be a common pathogenic mechanism in mammals [ 50].
Protocol modifications of sequencing experiments could modestly improve performance, such as the use of whole genome amplification [49], [50], but this can introduce loss of heterozygosity.
Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation.
"What are the moral implications of genome editing?" is the question that has been posed by the Nuffield Council on Bioethics regarding the new CRISPR-Cas9 mediated germ-line genome editing technique, which allows targeted modification of DNA sequences at the level of the germ-line, i.e. gametes (eggs and sperm).
Plasmid DNA is highly stable and flexible, allowing for the modification of plasmid sequences [ 14].
Enzymatic base modification of RNA sequences was originally discovered in the mitochondrial RNA of trypanosomes (Turelli and Trono, 2005).
The epigenetic modification of genic sequences is a common feature of allopolyploid genomes [ 12, 13, 41, 42].
The only known mechanism for a direct modification of DNA sequences after their synthesis is the methylation of nucleotides.
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