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Thresholds are typically chosen by ordering record pairs by weight and manually inspecting to determine the weight at which pairs were thought to be more likely than not a match.
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MSAs that did not meet these criteria were manually inspected to evaluate further manual editing (split alignments).
Additionally, each locus was manually inspected to assign curated genes.
For gaps with identical flanking sequences, insert size for mate-pair reads and signal pattern for optical molecules that span or flank these gaps were manually inspected, to identify redundant sequences that were then trimmed to close the gaps.
In addition, MS/MS spectra of major precursor ions unidentified by the Mascot search were manually inspected to assign amino acid sequences.
The orthologous tracts (LTR+NRR) were aligned and manually inspected to identify all substitutions that accumulated in both the LTR and NRR sequences, respectively, since speciation took place (Supplementary Figure 1).
The corresponding sequences were manually inspected to rule out sequencing or assembly errors.
Both the sets were manually inspected to prevent the mislabeling of the data.
Each trial was manually inspected to verify proper marker identification and the absence of movement artifacts.
Selected templates were manually inspected to choose those ones with the highest crystallographic quality and sequence coverage.
Final class-average images were manually inspected to determine their oligomeric state and tabulated to determine the oligomeric composition of each sample (Table 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com