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In some cases, novel function may come about with only a small level of sequence divergence of the protein coding region.
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They compose a large family (approximately 40 known members in the human system)[1] of small proteins which share a relatively low level of sequence identity, but which display a remarkable structural homology, since they all contain the same monomeric fold.
Peroxins show only a low level of sequence conservation.
In many comparative studies of chloroplast protein coding genes, the distance value for rps7 gene sequence was mainly small indicating low levels of sequence divergence [ 88, 89].
Overall, a high degree of sequence conservation among the Solanaceae was observed in accordance with previous small scale studies [ 6]; for up to 81% of the gene index sequences, significant matches at the nucleotide level could be found within the Solanaceae, consistent with the level of sequence conservation observed at the protein level.
DDiMAP is designed to search through relatively small regions of the genome at a very high level of sequencing coverage to identify and quantify genetic subpopulations.
The goal behind a genotyping scheme is to classify viruses by using a smaller sequence window that has levels of sequence variability that correspond to variability between complete genomes and that would give the same phylogenetic tree topology with high bootstrap values.
Although the majority of intergenic regions showed no significant sequence similarity between distantly related species, there may be a small subset of syntenic orthologs that have high levels of sequence similarity across a portion of the intergenic region.
It was previously observed that selfing species have generally lower levels of sequence variation than outcrossing species because of smaller effective population sizes [ 38].
We have studied the effect of different levels of sequence redundancy in the MSA, by calculating MI not only with the original data set of 348 sequences but also with a series of progressively smaller MSAs in which the highest level of identity between any two sequences was 98, 96, 94, 92, 90, 88, 86, 84, 82, 80%.
Phylogenetic analysis based on RVFV partial small and medium RNA sequences showed a low level of variation between isolates from humans, animals, and mosquitoes.
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