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This powerful approach has opened up new frontiers that overcome some of the metagenomic assembly limitations and culture biases.
This is likely an overestimate of the number of loci represented in our transcriptome due to de novo assembly limitations.
Despite these methodological and assembly limitations, some important trends regarding bovine segmental duplications emerged during our study.
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Although this approach remains the gold standard for sequence and assembly quality, limitations with respect to cost, labor-intensiveness and speed, which are largely due to the necessity of generating and arraying cloned shotgun libraries and isolating template DNA for sequencing, have fueled the demand for new approaches to DNA sequencing.
However, because of uncertainties in the assembly or limitations of aCGH resolution, these studies could not distinguish whether the recurrent CNV is mediated by a shared genomic structure in the hotspot region, characterized by a similar pattern of segmental duplications, or by truly independent events derived from a distinct genomic structure.
For every case of non-assembly fabrication, the limitations of the applicable AM processes are presented and further discussed.
Further, the local nature of PRICE assembly jobs (limitation of input sequences to those inferred to derive from local genomic regions based on paired-end information) was intended to avoid the chimeric misassemblies that would be expected to arise when applying reduced alignment stringency to a full dataset.
The proximal boundary of the duplication, identified in 243E20, is not assembled on chromosome 8 in the rheMac2 assembly, illustrating the limitations of using a whole-genome shotgun assembly for array CGH design and the importance of BAC sequencing in assembling complex genomes.
Differences between captured genes could be attributable to polymorphism, assembly defects, or limitations of CEGMA in distinguishing between paralogous genes.
The use of a comprehensive infectious agent database allows detection without the need for sequence assembly, however, a limitation of this technique is that that totally novel IA candidates could be missed if their expressed genes are not closely related to any known agent.
The increased proportion of undesired plasmids with nine-point mutagenesis compared with six-point mutagenesis suggests that the number of DNA fragments requiring assembly is a limitation of MUPAC.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com