Sentence examples for the alignment ratio from inspiring English sources

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).

At sequence identities ≥20%, the alignment ratio calculated by BLAST for the two domains of domain-swapped proteins differed less than 30%; at sequence identities ≥50%, the difference reduced to <10%.

Because the DS score is specifically designed for detecting DS, its MCC for distinguishing homologs (both DS and common homologs) from non-homologs is supposed to increase as the alignment ratio cutoff declines.

The alignment ratio and RMSD also varied with the sequence identity; however, because the variations were moderate, and it is reasonable that evolutionarily more distantly related proteins develop more structural differences, these results might just reflect the nature of the aligned proteins and should not be considered as a decrease in performance.

However, as the alignment ratio cutoff decreased, the number of common global homologs in the testing set decreased much more rapidly than that of DSCO pairs (refer to Figure S1) and the remaining DSCO pairs maintained high scores that became relatively higher and higher than the scores of the partial and low-similarity homologs remaining in the testing set.

However, these measures were not as effective in separating DS-related homologs from common homologs, as evidenced by the relatively low MCC and sensitivity for this part (MCCs<0.80 and average sensitivities≤0.88), which declined as the alignment ratio cutoff became lower (Fig. 2f).

In the experiments of Fig. 2, the alignment ratios of all protein pairs were uniformly calculated by FAST [30].

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).

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%.

Otherwise, its alignments are scored and the alignment ratios calculated.

To identify the related pathway names in two databases' pathway name lists (x and y), we iterate each name in the list x and search against all the names in the list y; for each name in x, we report the best hit in y. "Best hit" means that, for each name from x, when searched against all the names in y, the one that gets the highest alignment ratio is reported as the best hit for this round.