The phrase "alignment directly" is correct and usable in written English.
It can be used in contexts where you are discussing the specific manner in which alignment is achieved or addressed.
Example: "To ensure the project meets the required standards, we need to focus on alignment directly with the client's expectations."
Alternatives: "alignment specifically" or "alignment in a direct manner".
On the other hand, if only one method was able to align a molecule, we included this alignment directly regardless of the method.
It has been an established fact that the nano-filler extent of dispersion and alignment directly affects the mechanical properties of the composites [8, 9].
It is considered that the extent of crystallization and regular alignment directly determines the properties of nanofibers itself.
Sequence reads were mapped to the bTau6 build using the Burrows-Wheeler Aligner (BWA) (Li and Durbin, 2009), and resulting alignments directly visualized with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
As the 454 reads were shorter and the E-value of an alignment is directly proportional to the product of the lengths of the two aligned parts, we used for 454 read alignments an E-value cutoff of 10-7.
The mean values based on the MG-CFA with alignment are directly estimated from the model.
The combination of parameter k and parameter "match-core" determines the alignment, which directly affects the hit sensitivity.
For rpoB, rpsB, and dnaG, we used HMMER2.0 profile models and alignment functionality directly from AMPHORA, which applies a "non-strict" mask designed to improve the alignment quality.
Here, we introduce a technique that does not rely on such alignment but directly measures the statistical structure inherent in the arrangement of labeled patches and of cortical responses.
High-quality data sets of smaller particles (about 300 kDa or less) collected using 50 to 100 e−/Å exposures are currently not available to demonstrate the improved particle alignment more directly with experimental data.
We described an approach to evaluate parameter sets based on the inner and outer score distributions and we note that already available methods to optimize other alignment-based scoring systems, e.g. for homology modeling and of protein (structure) alignment can directly be applied to ALPS.
