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Therefore, other important information across prokaryotic genomes, such as genomic function and genomic structure, should also be considered for orthologous genes identification.
First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information.
In the first step, we compute orthologous genes by considering sequence similarity, genomic function, and genomic structure information.
We can see that many special genes are reduced by considering genomic function and genomic structure information.
Sequence similarity is calculated by BLAST, whereas genomic function and genomic structure are estimated by COG and operon annotation, respectively.
From our perspective, identifying over represented GO terms can provide insight into regional genomic function, and while statistical methods of measuring GO term distribution vary, we have adopted a commonly used method based on the hypergeometric distribution [ 12].
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In addition, the ChIP-chip and ChIP-seq technologies enable researchers to investigate the distribution of the histone marks (and other proteins) on the genome at a high resolution, which led to the discovery that the binding patterns of the proteins and histone marks over the genome are also highly informative in predicting genomic functions and annotations [ 13, 15- 17].
Our present studies provide a useful tool for future research on genomic functions and molecular pathogenesis of DHAV-3.
Genome-wide studies of histone modification patterns have shown that specific histone modifications are associated with specific genomic functions and that these patterns are altered in cancer.
Comparison of the genome of a metatherian (marsupial) with those genomes available for eutherian (placental) mammals offered the prospect of insight into genomic function, organization, and evolution among mammal lineages.
Recent developments in epigenetic-based technologies, including miniChIP chip, will continue to pave the way in expanding our knowledge on the mechanisms of epigenetic inheritance, gene transcription, and genomic function in developmental processes and tissue homeostasis.
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