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Most incomplete alignment boundaries (73% for BLASTP, 76% for SSEARCH) were from alignments in the lowest two identity quartiles.
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The most overextended alignments (>40 residues, Fig. 2) decreased by 2217 alignment boundaries, whereas the most incomplete alignments increased by 399 boundaries.
Most (73%) of the realigned incomplete alignment boundaries fall into the bin (orange).
A complete alignment indicates low divergence, whereas an incomplete alignment indicates substantial divergence.
In contrast, incomplete alignment boundaries are more common in low identity alignments, whereas overextended alignment boundaries are more common in high identity alignments.
In this more closely related set, the percentage of overextended alignments increases to 8% for BLASTP and 10% for SSEARCH and incomplete alignment decreases to 8% and 5%, respectively.
Restricting the analysis to the top 25 homologs further decreases incomplete alignment to 2%, whereas increasing overextension to 11%.
Incomplete alignments can occur when homologous domains are evolutionarily distant, so that the alignment captures only the most conserved regions of the homology.
Incomplete alignments that missed spacer regions due to deletions or genomic translocations were not used in our analysis.
Incomplete alignments are another example of inadequate alignment sensitivity.
Incomplete alignments had negative boundary errors and overextended alignments had positive boundary errors.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com