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The distance between PSEUDO loci and flanking genes was found to be larger compared to the LNCRNA set, while the LNCRNA loci were found in divergent orientations more frequently than a convergent one.
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Neither conserved in composition, nor unified by common evolutionary ancestry, RNA degradosomes nonetheless can be found in divergent bacterial lineages, implicating a common requirement for the co-localisation of RNA metabolic activities.
In teleosts, conserved brain-specific miRNAs are found in divergent species (Soares et al. 2009; Xia et al. 2011; Bizuayehu et al. 2012b; Zhu et al. 2012; Xu et al. 2013).
A similar situation involves Muscina levida (Harris), where a number of differences were found in the single genetically divergent specimen (Additional file 3), which was consequently renamed Muscina sp. 1 (Table 1, Additional file 1).
When two or more paralogs were found in a species, the most divergent of the paralogs was removed from the alignment.
Direct orthologues of some of these divergent SoxBs were found in the genome of the hydrozoan cnidarian Hydra magnipapillata in our analysis (Fig. S5, based on the alignment in Fig. S2D).
Divergent associations were found in patients based on their HPV status.
More divergent sequences were found in the Uncharacterized Protein Family entries of UNIPROT Knowledgebase: UPF0328 (interD), UPF0329 (interAE and interB).
For five of the 700 loci, three divergent sequences were found in the EST library (15 sequences total).
Divergent homologs were found in Streptomyces wedmorensis, Streptomyces fradiae and one strain of Pseudomonas syringae (all probably fosfomycin kinases), and Shewanella denitrificans.
Divergent haplotypes were found in Cabullona (CAB) and Agua Prieta (PRI), both in the Yaqui River basin, as shown by the number of segregating sites (S) and average number of nucleotide differences (k) (Table 2).
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