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The resulting mutation list was compared with the WHO mutation lists for HIVDR surveillance [ 21, 22].
We then used a second customized script to perform a series of pairwise comparisons using the mutation lists for each of our three libraries.
After identifying candidate mutations for the current study, we randomly selected 15 sites from the resultant PB306, HK104, and PB800 candidate mutation lists for confirmation analysis using PCR and ABI capillary sequencing.
While our comparison strategy using the individual libraries should, at least in theory, provide complete mutation lists for each genotype, our low coverage prompted us to take a second complementary approach.
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TDRM was defined according to the mutation list published for surveillance of transmitted drug resistance as recommended by the World Health Organization [ 11].
The primers are used for mutation listed in Table 2. Disruption of dr0615 did not show a growth defect (data not shown).
COLO-818 is one of the two cell lines from Table 1 which does not have sequencing data in COSMIC, this cell line mRNA was sequenced by (Klijn et al., 2015) and it was found to contain C135R TP53 mutation, this is exactly the same mutation as listed for COLO-818 in Table 1.
The resistance associated mutations were identified according to the surveillance drug resistance mutations list recommended for drug-naïve patients.
The list of mutations in the form of chain name, residue index, and mutation amino acid should be given in the Mutation List text box.
Using a document classifier, the abstracts containing mutations without any impacts are removed and the remaining abstracts are classified into two groups of disease related and non-disease related documents, after which extracted mutations are listed for each group.
Nucleotide sequences are listed for primers used for exon-based validation of somatic mutations listed in Table 1, and for all exons of the MAX gene.
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