The phrase "alignment ratio" is correct and usable in written English.
It can be used in contexts related to measurements, comparisons, or assessments of alignment in various fields such as engineering, design, or data analysis.
Example: "The alignment ratio of the components was crucial for ensuring optimal performance in the machinery."
Alternatives: "alignment coefficient" or "alignment proportion".
When the structural alignment ratio cutoff was lower than 98%, the MCC values of most methods approached zero (Fig. 2c).
The average alignment ratio calculated by the proposed method for main domains were 7% smaller than that for swapped domains.
The MCC values were all lower than 0.54, and they declined dramatically as the cutoff of the structural alignment ratio became lower.
In this way, all alignment methods and similarity measures were assessed on an equal basis, no matter at which alignment ratio cutoff point.
As shown in Fig. 2c, at the 100% alignment ratio cutoff, which actually means that no protein was filtered out from the testing set, the best MCC value achieved was only 0.54 by SARST [34].
To rule out the effects of various protein sizes, in implementation the alignment size was normalized by the protein size with Formula 3 and was thus called the alignment ratio (unit: percentage).
In the experiments of Fig. 2, the alignment ratios of all protein pairs were uniformly calculated by FAST [30].
As shown in Figure S3, the average difference of the alignment ratios calculated by this method for the two domains in a DSCO pair with <10% sequence identity was 9%.
Detailed analyses revealed that the alignment ratios calculated by the proposed method for the two domains of DS-related proteins differed more as the sequence identity decreased, although the differences were not very large (<9%; see Figure S3).
For a DSCO pair and a pair of common homologs, when SARST reports similar alignment ratios for both cases, usually the RMSD of the former will be much larger than that of the latter, resulting in very different structural diversity (S-div) [41] values.
Otherwise, its alignments are scored and the alignment ratios calculated.
