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Optimisation of the sensor design, the modifier content and the immobilisation and hybridisation times was attained using a simple nucleotide sequence.
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The H58 lineage is highly clonal and differentiated from other haplotypes using a simple single nucleotide polymorphism based typing scheme [ 14], and is associated with high levels of multidrug resistance [ 13, 15].
We simulated sequences using a simple model of nucleotide evolution along a four-taxon star tree with two long and two short terminal branch lengths (Fig. 1a).
Here, we performed a simulation study of the formation of unidirectional overlapping genes using a simple model of nucleotide change and contrasted it with empirical data.
Using a simple model of random nucleotide change, we show that overlapping genes formed after the elongation of the 3′-end of gene 1 are twice as frequent as those originated by the elongation of the 5′-end of gene 2. We suggest that this is a consequence of the redundancy asymmetry between start codon and stop codon sets.
To test whether the formation of an overlapping region caused by elongation of gene 1 or gene 2 was equally frequent, we performed a computer simulation using a simple neutral model for the accumulation of nucleotide changes.
By default, only nucleotide sequences are presented, but the protein view is accessible using a simple switch at the top of the page.
The assembled data were then queried for the presence of microsatellites using a simple python script using all possible sequences combinations of di-, tri- and tetra-nucleotide repeats, with at least eight perfect repeats.
SNPs were called using a simple thresholding.
Data were collected using a simple questionnaire.
MOVs are assessed using a simple algorithm.
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