The phrase "alignment it uses" is correct and usable in written English.
You can use it when discussing the specific type of alignment employed by a system, method, or process.
Example: "The software's effectiveness largely depends on the alignment it uses to integrate various data sources."
Alternatives: "the alignment it employs" or "the alignment it applies".
bigWig uses more memory for indexing than Tabix but is still reasonably small: at 160 million alignments, it uses 2 GB to finish the run.
Since keeping the ball on the ground is an unlikely option — Pittsburgh gives up 66.5 rushing yards a game — New England may stick to the shotgun alignments it used in Miami.
Mulan [ 9] produces an annotated alignment, but it uses only pairwise alignments of each sequence with a reference sequence; multiTF identifies conserved TFBS in the Mulan output, and displays the result pairwise using rVista [ 11].
During the 1960s and 1970s, M-14 was moved to the freeway alignment it currently uses; sections of the former route are still maintained by the Michigan Department of Transportation MDOTT) as unsigned highways.
This program is different from most other alignment programs in that it uses an evolutionary model to place insertions and deletions, with the result of minimizing the overalignment of nonhomologous regions.
It uses global alignment, which is the total alignment score of the overlapping region.
We note that XtalPred was updated in mid-2007 and it uses sequence alignment against recent contents of the PDB and nr databases, which helps to keep its predictions more up-to-date.
These pairs are identified using megablast, which, since it uses approximate alignments, is rapid even for large datasets.
It uses blastx alignments to build a complete gene model from the hits, and is particularly useful in low-coverage genomes with low quality regions, frame shifts or gaps, where ab initio gene predictors generally predict no or incorrect gene models.
It uses multiple alignments and a merging process in an attempt to resolve a given read's origin.
