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Of the functional motifs within this region, the most universally conserved is the DBS (Figs 3 and 4).
Adaptation requires the products of the cas1 and cas2 genes in vivo and these are the most universally conserved of all the cas genes (Makarova et al., 2006).
At higher resolution, we observe an interesting mutational trend for YUB.2-MUS.A5 and YUC.1-MUS.B2: a tendency to accumulate non-synonymous substitutions immediately adjacent to the most universally conserved amino acid residues (Table 4).
Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway.
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In contrast to the variation in inner kinetochore protein repertoires, homologs of outer kinetochore components including Ndc80 and Mis12 are almost universally conserved in most insect orders.
They constructed a frequency profile from a large set of universally conserved proteins that most biologists believe to be homologous.
To produce their simulated sequences, K&W constructed a frequency profile from a large set of universally conserved proteins that most biologists believe to be homologous (including Koonin, Wolf, and their reviewers [ 2]).
Although most organisms have a similar set of universally conserved biased codon pairs, some organisms use slightly different sets (e.g. N. equitans) and some have a very small number of biased codon pairs (e.g. B. aphidicola, C. blochmannia).
The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs).
The most straightforward interpretation for the relative lack of universally conserved miRNAs between P. tricornutum and other organisms is that all miRNAs in P. tricornutum are rare due to its small genome size, although scenarios that P. tricornutum contains novel miRNAs that have no sequence homology with all known ones cannot be ruled out.
To observe the range of QIPP scores that might be expected from the most highly conserved CDS we examined a subset of universally conserved genes [3].
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