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Novel TUs with length < 150 bp or average expression of < 2 reads per base were excluded from further analysis.
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Gaps and ambiguously aligned bases were excluded from the 55-taxon alignment resulting in 1,486 unambiguously aligned sites.
Seven sequences less than 400 bases were excluded from the analyses, and the mean length of those remaining was 647 bases.
Poor-quality (<15) bases were excluded from error estimation as they had been previously masked with Ns.
Individuals living in institutions such as hospitals, prisons, mental health institutions and military bases were excluded from the study.
Second, although the mismatched bases were excluded from data analysis, they provided an empirical estimate for single-read sequencing error rates.
Also relating to generalizability, the findings presented here apply to older Canadians included in the NPHS sampling frame (for example those living on aboriginal reservations, in remote Northern communities and on military bases were excluded from sampling).
Non-protein coding genes (e.g. pseudogenes and rRNA genes), incomplete genes, coding sequences with less than 100 codons, extra-chromosomal sequences and sequences containing ambiguous bases were excluded from analysis.
When the N bases were excluded from the assembled sequences, the content of the repetitive sequences was calculated to be 42.3 47.7% of the entire I. trifida genomes, which is lower than the contents in other plant species such as Lotus japonicus (56.8%), potato (64.2%), and tomato (68.3%).
Sequences with ambiguous bases are excluded from the analysis.
Nucleotide positions in which no base call was made or in which the forward base call was different from the reverse base call were excluded from further analysis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com