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Therefore, we defined x and y here as mapped reads per kilobase of a transcript to avoid bias of sequence length.
Firstly, we selected protein-coding genes that were associated with only one type of annotated transcript, to avoid ambiguity due to splice variants.
This array was designed by us, and each probeset is composed of an average of 11 probes dispersed along the transcript to avoid any impact of polymorphism on detection.
The results were similar when we restricted the analysis to genes encoding a single transcript to avoid any possible biases due to multiple read mapping or when we employed the maximum TE in 90 nucleotide windows.
The pairs of primers used to analyse the expression of MtN5 in hairy roots were specifically chosen at the 3′ end of the transcript to avoid the amplification of sequences derived from the hp construct itself.
If there is an annotation for this functional term, that term's position in the vector is set to 1, otherwise it is set to 0. Considering the hierarchical structure of function annotations, we used only the sub-root level annotations (the direct children of biological process/molecular function) for each transcript to avoid redundancy.
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RF4 is considered to recognize and bind orf352-containing transcripts and promote the degradation of orf352-containing transcripts to avoid ORF352-mediated programmedprogrammed cell death and consequent male sterility (Luo et al. [2013]).
Our data support the conclusion that only ~30% of such variants lead to significant reduction in expression of the impaired allele, suggesting that either NMD acts selectively only on specific transcripts or that there are additional, unknown mechanisms that allow transcripts to avoid it.
Convergent overlapping transcripts were excluded from the quantification of antisense transcript levels to avoid potential confusion between sense and antisense transcripts in these cases.
Maternally deposited coding transcripts tend to avoid some target sites for highly abundant maternal microRNAs (with respect to zygotic transcripts).
MicroRNA primers were designed at the 5' regions of the transcripts as to avoid potential mis priming due to the sequence variation observed at the 3' ends of microRNA transcripts.
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