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We show that these assemblies exhibit modest but non-negligible levels of sequencing error, which, if ignored, can produce biases in downstream phylogenomic analyses.
Note that because even very low levels of sequencing error would affect these conclusions, the sequences for the regions involved were verified as discussed in Supporting Methods Text S1.
In addition, low-coverage assemblies necessarily have elevated levels of sequencing error that is, miscalled bases and erroneous insertions and deletions, which might otherwise be corrected through redundant sequencing of the same genomic region.
While such approaches do not necessitate reference or mediator genomes, at the current levels of sequencing costs they are less affordable for routine use in individual laboratories [10], [12].
We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data.
In contrast, varying levels of sequencing noise and BRAFV600E signals were often encountered when biopsied melanoma tissues were sequenced.
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Data reported here also indicate high levels of sequence divergence within Glyphorynchus.
Interspersed between their conserved cysteine residues are constrained loops that possess high levels of sequence diversity among knottin family members.
The members of this enzyme superfamily display low levels of sequence identity while possessing a common fold and active site.
Shading indicates levels of sequence conservation (100% conservation: white on black; 75% conservation: black on dark grey).
The 16S rRNA gene sequence of the isolate NFH5 showed high levels of sequence similarity with members of the genus Arthrobacter (Fig. 2; Additional file 1: Figure S2).
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