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In the studies of statistical analysis for protein evolutionary family the following two basic hypotheses were recognized widely, which were derived from the empirical observation of sequence evolution [2].
The observation of sequence heterogeneity between C. parvum and C. hominis at the Cops-1 locus suggested potential taxonomic utility for the gene in subtyping of strains.
The observation of sequence conservation suggests that these phages belong to the diverse T4-like phage superfamily but somewhat distant to the archetypal member of the group.
Along with the observation of sequence similarity to a putative donor, this led to the hypothesis that a capsule-switching recombination had also altered the linked penicillin-binding protein (PBP) genes that determine susceptibility to such antibiotics (Moore et al. 2008).
This was established by observation of sequence characteristics of the upstream regions of the direct category genes: high A+T content, A/T richness of the most frequently found 5- and 6-mers, and a high rate of occurrence of 2 6 nt heteropolymeric A/T sequences.
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However, the observation of sequences related to PV-1 from numerous hydrothermal systems suggests FeOB may be more widespread than is currently recognized [38], [39], [40].
We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation.
The mitochondrial targeting of MSH1 plus initial observations of sequence similarity between MSH1 and mtMutS formed the basis of early conclusions that the two genes were orthologous [ 15].
Initial understanding of miRNA-mRNA target recognition came from observations of sequence complementarity between lin-4 and multiple conserved sites within the gene lin-14 3′-UTR [ 35].
Within-sample analysis of R. solani AG-3 from potato identified probable recombinants through observations of sequence homoplasy in the networks of both pP42F (point a) and pP89 loci (points a, b, c, d, and e).
Seismograms of earthquakes with M > 6 revealed that this is the first observation of a sequence of deep-focus earthquakes with magnitudes larger than 5.5 within several minutes along the Izu Bonin arc (Fig. 4).
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