The phrase "alignment quality for" is correct and usable in written English.
It can be used in contexts where you are discussing the effectiveness or accuracy of alignment in various fields, such as data analysis, machine learning, or project management.
Example: "The alignment quality for the new algorithm significantly improved the overall performance of the system."
Alternatives: "alignment effectiveness for" or "alignment accuracy for".
The performance evaluation shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed.
Using the above measures, CUSHAW2 is shown to be among the highest-ranked aligners in terms of alignment quality for both the SE and the PE alignment for a variety of error rates and varying amount of indel errors.
Hit lists comparable to the Gaussian shape overlay optimizer ROCS can be obtained 100-times faster with only a small loss in alignment quality for smaller and relatively inflexible molecules.
Despite the dot plots showing high alignment quality for both, the FRC scores them very differently (see FRCs in Document S1).
The alignment quality for each individual block was then measured using the Block Column Score (BCS) described in Methods. Figure 6(A D) shows the distributions of the block scores obtained by each MSA program for each block attribute.
Here, we assessed the resulting alignment quality for different values γ=7,8,9 and 10 for the ExpaRNA algorithm.
The model incorporates read and alignment quality, adjusts for non-uniform read distributions and accounts for an experiment-specific fragment length distribution in case of paired-end reads.
Sequence and alignment quality metrics for each patient and PE pulse are available in Additional file 1: Table S2-S3.
LocARNA and SPARSE show qualitatively similar performance; across the entire range of sequence identities, we observe a largely constant quality offset, where both tools maintain a high alignment quality even for low sequence identities.
Alignment quality control for minimum percent identity and bi-directional coverage is then performed to remove sequences not meeting these criteria (these values are user-specifiable parameters of the algorithm).
Whereas the gap size strongly influences plasmonic coupling, the overall alignment quality is crucial for homogeneity.
