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MSAs that did not meet these criteria were manually inspected to evaluate further manual editing (split alignments).
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.
For those proteins with only one matching peptide, the MS/MS spectra were manually inspected to validate the protein identifications (see Text S1).
Clustering of the RAxML bootstrap trees using PhyloSort resulted in a "unitree" set of 68 phylogenies each of which was manually inspected to verify the topology.
Final class-average images were manually inspected to determine their oligomeric state and tabulated to determine the oligomeric composition of each sample (Table 2).
Passing MS/MS spectra were manually inspected to be sure that all b- and y- fragment ions aligned with the assigned sequence and modification sites.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com