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From the 1032 SNV, we excluded insertion or deletion variants to avoid potential technical difficulties in genotyping.
To further demonstrate the feasibility of applying Hsp104 to reversing disease in humans, it will be essential to develop substrate-optimized Hsp104 variants to avoid off-target effects.
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The HIV-1-B Nef peptides that were reactive in the ELISpot assays were compared by testing k-mers (with k = 8, 9, 10 AA) that had the same HIV-1 HXB2 strain coordinates; in brief, a consensus k-mer was compared to its variant k-mer(s), with k being of the same length for the consensus and variant to avoid the creation of gaps when aligning the 2 k-mers.
In the comparison of annotation tools here, we restricted each tool to report just the most severe consequence annotation for each variant, to avoid comparisons becoming too unwieldy.
To enable quantitative comparison of PREs and their variants, and to avoid the problem of genomic position effects, we adapted the ΦC31 site-specific integration system to make it suitable for comparative studies of PREs at the same genomic location [ 46].
In a practical application, one will most likely rely on a combination of variant callers to avoid the biases of a single method.
Reads mapped with mapping quality greater than or equal to 10 and bases with base quality greater than or equal to 17 were used for variant calling to avoid false positives due to errors in read alignment and sequencing errors.
Primers which were designed against genes that are currently tested in this laboratory by Sanger sequencing were also manually compared against our own variant lists to avoid common sequence variations that might interfere with primer binding.
Putative PCR priming sites were selected by RainDance Technologies using genome build hg19/GRCh37 with custom software and compared automatically with public variant databases to avoid nonspecific priming and common single nucleotide polymorphisms.
For all strains prototrophic variants were used to avoid the necessity of supplementing the media with amino acids and/or nucleic bases.
We sought to identify pharmacogenetic interactions that were based on a single drug and single genetic variant and wanted to avoid drug drug SNP interactions.
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