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Anomalous conformational effects exerted by the Alu-Yi6 element on genomic structures were revealed by the blockade of sequencing by polymerase across the Alu-Yi6 element inside a free-ended template (Figure 6A), which was surmountable by placing the template into a circular vector or by excision of the poly-A tail from the Alu-Yi6.
CW-CMS-specific genomic structures were found in the region around the rpl5 locus with exclusive genomic recombination involving the orf288 locus.
A total of 96 SNPs and 25 Indels were predicted between 93-11 and PA64S, but the differences in their overall genomic structures were rather conservative, in comparison to the report that the sequence arrangements of two normal cytoplasms from maize were never in parallel [ 11].
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The task becomes more complicated if genomic structures are similar.
Differing genomic structures are also apparent on alignments of L. johnsonii strains with the closely related L. gasseri (Figure 2) (4, 11) indicating rearrangements in this group of bacteria can occur frequently and 'X-shaped' inversions across the replication terminus between species of the acidophilus group have been documented [15].
A schema of these genomic structures is shown in Figure 1(a).
Their genomic structures are similar to those of their human counterparts, but their sizes have evolved differently.
MDV is a highly cell-associated herpesvirus with lymphotropic properties but its molecular and genomic structures are similar to Alphaherpesvirinae subfamily [ 1].
Interestingly, ALDH1A1 and ANXA1 genes map to a common chromosomal region in both species and the genomic structures are well conserved among human, mouse and rat.
The role of the UGT genes in metabolizing myriad xeno- and endobiotic compounds suggests that natural selection may have played an important role in shaping their variation; however, the effects selection might have on such unusual genomic structures are unclear.
This finding is consistent with the probe selection method used to optimize the assay, which requires that the species-specific probes be a near match to the human array (allowing for only a four base mismatch), meaning that conserved genomic structures are going to be preferentially retained and that the analyses of non-human genomes are going to be limited to these regions.
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