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While this distribution basically decayed in a fashion similar to the macroscopic and microscopic inversions between the human and chimpanzee genomes [ 6], extremely short inversions were less frequent.
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In particular, comparative genomics between populations and between closely related species have revealed the occurrence of numerous inversions in genomes including small-size (microscopic) inversions [ 4- 6].
In addition to macroscopic and microscopic inversions, a large number of ultramicro inversions, ranging from five to 125 bp, were detected between the human and chimpanzee genomes using our method (Table 1).
It can be a cause for the false positives in the larger inversions as a single alignment or a string of local alignments (microscopic inversions) than ultramicro inversions.
The ultramicro inversions are also distinguished from larger microscopic inversions that are detectable as a single alignment or a string of local alignments, in that the exact boundaries of ultramicro inversions can be identified easily within the local alignment.
Although several methods have been developed to identify these inversions, they focus only on the macroscopic or microscopic inversions which are inversions large enough to be detected as a single alignment or a string of local alignments [ 6].
While the ultramicro inversions as well as the macroscopic and microscopic inversions were spread throughout the human genome [ 6], the density of inversions was significantly different on chromosome Y compared with that on the autosomes.
Ultramicro inversions may also be spread across the human and chimpanzee genomes because the size distribution of the macroscopic and microscopic inversions decays as the size of the inversions increases [ 6].
While our inversion-identification method was helpful for examining the impact of microscopic inversions, this method is also applicable in fine tuning genome alignments by distinguishing ultramicro inversions from nucleotide substitutions and indels.
With this definition, most of the "ultramicro" inversions are expected to be smaller than the "microscopic" inversions which are identified as a single alignment or a string of local alignments.
Traditional cytogenetic approaches have long been able to identify microscopic inversion events, but discovery of submicroscopic events has remained elusive and largely ignored.
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