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For example, reads that map to the boundary of a new insertion of a mobile element that is multicopy in the original genome will have multiple alignments to the reference sequence for the portion overlapping the mobile element.
Significant A → G gradients in opposite directions were also observed in each half of the genome portion overlapping the SSC region and ~7kb of the other tail end, respectively, of both the inverted repeats (A1 → A1-C) for all species from these six categories.
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Our linear regression analyses on the nucleotide compositions of the non-coding regions and the synonymous third codon position of coding regions, between pairs of replication origins, reveal the existence of significant adenine to guanine deamination gradients in portions overlapping the Small Single Copy (SSC) and the Large Single Copy (LSC) regions between inverted repeats.
The Several reasons could account for the small portion of overlapping.
There's a considerable portion of overlapping hits between each pair of results, but none of the programs produce completely identical HGT predictions.
By contrast, the assembler we compare with produces a variety of output types: first, portions of overlapping reads are assembled into "contigs" representing putative exons.
We compared the two sets of ESTs to identify conflicts, in which pairs from each EST set share a significant portion of their sequence but cannot be aligned over another overlapping portion.
This compromise came about primarily as a result of the work of Charles Lapworth, the English geologist who in 1879 proposed the designation Ordovician System for that sequence of rocks representing the upper part of Sedgwick's Cambrian succession and the lower (and generally overlapping) portion of Murchison's Silurian succession.
We applied this procedure to every 500-year overlapping portion of the record, thereby producing a unique threshold for each subsample.
Ideally, a perfect alignment of a pair of quadrilaterals means a unity ratio between (A_{hat {Q}Q}) and A Q, where (A_{hat {Q}Q}) is the area of the overlapping portion of (hat {Q}) and Q and A Q is the area of Q.
If the 3' end overlapped an adjacent gene, the overlapping portion was removed.
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