The phrase "alignment quality is" is correct and usable in written English.
It can be used when discussing the standard or effectiveness of alignment in a specific context, such as in design, data analysis, or project management.
Example: "The alignment quality is crucial for ensuring that all components work together seamlessly in the final product."
Alternatives: "quality of alignment is" or "alignment standard is".
Alignment quality is critical to phylogenetic analysis because the alignment is a hypothesis concerning the homology (common ancestry) of the residues at the same position in each of the aligned sequences (positional homology).
Thus we do not expect that alignment quality is a concern.
To increase the accuracy of these applications, homology detection sensitivity and alignment quality is crucial.
Below 35% sequence identity, homolog detection and sequence alignment quality is known to decline (Rost, 1999).
Whereas the gap size strongly influences plasmonic coupling, the overall alignment quality is crucial for homogeneity.
The alignment quality is assessed using two standard measures: alignment sensitivity and precision, as described in Section 2.4.
The intact foldback arms from 13 of the 16 gene-similar MIRNA loci were aligned with up to three gene sequences, and alignment quality was displayed using heat maps (Figure 5; MIR163, MIR163 and MIR447c were not included).
Sampled sequences are aligned using MUSCLE [ 44], sequences with low alignment quality were manually removed.
These proteins were aligned using T-Coffee (Notredame et al. 2000) and the alignment quality was assessed using Transitive Consistence Score (TCS, Chang et al. 2015).
Based on these calculation results, the alignment quality was optimized and the whirling vibration characteristic under different alignment conditions was calculated.
BLOSUM62 scores indicative of alignment quality were averaged over a sliding window of 3 amino acids (i.e. the score at each position represents the average of it and each residue on either side).
