Sentence examples for alignment ratio and from inspiring English sources

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.

As expected, the DS score is relatively weak at binarily classifying homologs and non-homologs (Fig. 2d), for which the MCC was 0.57 at a 100% alignment ratio cutoff and gradually increased to 0.71 as the cutoff decreased to 85%.

All the alignments were carried out with a minimum alignment ratio of 0.93, and the minimum size of alignment of 20.

Subsequently, BLAST registered higher MCC values at lower structural alignment ratio cutoffs than at the high cutoffs, and it achieved the highest MCC of 0.46 at the 85% cutoff; nevertheless, it was still inadequate to serve as an accurate DS-detecting method.

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).

Co-orthologous genes matrix identified using the alignment ratio suggested close association of Citrus clementina, Citrus sinensis, and Citrus reticulata, as they belong to the same phylogenetic clade.

In the experiment of Fig. 2c, at a high structural alignment ratio cutoff, only those DSCO pairs with small swapped domains and common homologous pairs with a small number of non-superimposable residues were eliminated.

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).

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.

When the structural alignment ratio cutoff was lower than 98%, the MCC values of most methods approached zero (Fig. 2c).