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Draft sequences were visually inspected to remove introns not needed to maintain an open reading frame, and to identify a stop site for proteins judged to be a fusion of two adjacent proteins.
The output was manually inspected to remove false output entries.
The normalized data were manually inspected to remove signals originating from solvent adducts and isotope peaks.
The lists of significant biological process terms were manually inspected to remove redundant terms.
The list of significant GO terms was manually inspected to remove redundant terms.
Output sequences were manually inspected to remove false positives composed of tandem repeats and other non-TRIM sequences.
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Since the Oryza genome is riddled with repetitive elements and their remnants (IRGSP 2005), all flanking NRR sequences were carefully inspected to identify and remove any kind of repetitive sequence that could be detected.
Additionally, the alignments were manually inspected to find and remove columns where only one individual contained multiple differentiating sites adjacent to each other.
The raw data were inspected visually to remove any spurious samples as much as possible resulting from loss of lock due to the satellite propellant saving option and satellite movement.
MUSCLE alignments were inspected visually to remove sequences that were obvious alignment errors.
TC specific genes were inspected manually to remove duplicates and those with < 70% coverage to yield a total of 4,283 unigenes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com