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The labeling reaction is performed under denaturing conditions to provide high labeling yield, minimal sequence bias [ 26], and consistently reproducible efficiency for every miRNA sequence [ 31, 32].
Agilent microarrays use a single-color array protocol and combine a direct labelling method with innovatively designed, in situ-synthesized probes that have minimal sequence bias [ 3].
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The remaining IAP-derived 19mers have minimal downstream sequence bias, and likely represent RNA degradation products.
Many of those in the same orientation have a 5' U and minimal downstream sequence bias, suggesting they represent p-piRNA degradation products, while most reads in the opposite sense were found to have a bias towards A 10nt downstream of their 3' termini.
Dimerization was suppressed by removing a TERT domain linker with atypical sequence bias, which did not inhibit cellular or minimal enzyme assembly or activity.
Additionally, as the loci examined by SNP analysis are typically characterized by minimal sequence differentiation, these loci may be relatively immune to amplification bias as their amplification efficiencies would be roughly equivalent.
The oligonucleotides were designed with sizes ranging between 65 69 nucleotides, a minimal Tm window, bias towards the 3'-ends of transcripts, and minimal sequence similarity to other genes [ 58].
However, a clear sequence bias is evident.
we run the risk of incorrectly adjusting for biological sequence bias, rather than technical sequence bias.
The overall stability of TR coverage across the single-copy regions of the genome (evenness of the red line across fig. 1) suggests that sequencing bias is minimal.
Clearly, to solve these problems, one needs to transform the highly non-uniform read coverage along the genes into a more uniform one by effectively correcting the aforementioned technical biases in the current RNA-seq methods, or relies on a better sequencing technology with minimal read bias, or capable of sequencing transcripts in their full-length.
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